Updated as of 8/1/2017, thanks to everyone for the new information
Bug type: Text Errors leading to Functionality Issues/Missing Monster Types
Brief bug summary:
With the monster collection event going on right now (and after participating in a previous thread related to bugged monster collection), I've been sifting through my collection list to see what I should aim for along with the event monsters. I've found several monsters that seem to be entirely uncollectable for one reason or another. If anyone can confirm that they have collected these monsters, I'd be curious to know about it. These monsters include:
Zakum1 (Listed under El Nath, Page 3, Row 5, Column 4, this entry refers to a version of Zakum that cannot be fought through normal gameplay anymore. This entry is decidedly broken and CANNOT be collected, and hasn't been available for at least year as far as I can tell)
Seductive Violent Primitive Boar (Listed under Ludus Lake, Page 3, Row 2, Column 2, Elite Monsters no longer spawn with the prefix Seductive. Apparently it was replaced with the "Charming" prefix. However, I cannot confirm if killing a Charming elite version of this monster can collect it yet, more testing required. Ideally, this would just be changed outright to Charming to avoid any future confusion)
KO Chief Qualm Guardian (Listed under Temple of Time, Page 1, Row 2, Column 4, See above, same case with the KO elite monster prefix, which was apparently folded into the "Overwhelming" prefix. As before, more testing required to see if an "Overwhelming Chief Qualm Guardian" counts for the Monster Collection)
Seductive Chief Oblivion Guardian (Listed under Temple of Time, Page 1, Row 3, Column 4, see above)
KO Steel Xenoroid EX (Listed under Edelstein, Page 2, Row 4, Column 3, see above)
Seductive Alloy Xenoroid DX (Listed under Edelstein, Page 2, Row 5, Column 2, see above)
Magic-resistant Commanding Possibly-Evil Seal (Listed under Near Victoria, Page 1, Row 5, Column 1, may in fact be possible at this time. According to AlexF, he has collected this very monster recently. More testing is required, but this is promising. Even still, as with the Seductive and KO prefixes, it would be ideal if the text was corrected to "Magic Resistant Commanding Possibly-Evil Seal" (punctuation and capitalization exact) once and for all)
Charismatic Ripe Wolfruit (Listed under Arcane River, Page 1, Row 5, Column 4, this prefix does not exist and I can find no evidence that it ever has. It remains uncertain what prefix it is supposed to have (possibly "Charming"?), or whether any of the existing prefixes will allow it to be collected. Much the same as the Seductive, KO, and Magic Resistant monsters above, this should be corrected to any currently available prefix for clarity's sake. Additionally, there are those that have collected this monster. By all evidence, this occurred during the time period most Elites were bugged to display ??? as their prefix, and the Monster Collection happened to display the same for the Wolfruit. Unless you have collected this monster AFTER these issues had been fixed, please don't make a note of it)
Reindeer (Listed under El Nath, Page 3, Row 1, Column 2, this enemy shares an exact name with a different monster found in Mu Lung (under Mu Lung Garden, Page 1, Row 2, Column 1). There is suspicion that this is causing an error where the Lion King Castle monster cannot be collected itself)
The Monster Collection has been understood by most to rely on exact-name matches between creatures killed and what is listed in the Monster Collection itself. This works normally in most cases, but some oddities tend to happen by the nature of this design, and a lack of foresight in naming certain monsters. For example, it is known that Magnus can be collected in FriendStory during the scene where you hit gym teacher Magnus with soccer balls because the two share a name. It is known that the Chief Cygnus Knights (Mihile, Oz, Eckhart, Hawkeye, and Irena) can be collected during certain events where they appear in different forms (in my case, I collected half of them during Sengoku High runs), again because they happen to share the same exact name. And perhaps in the oddest version, during the Tangyoon's Kitchen party quest, you can summon a creature named Snowman that resembles the kind you might make in winter, and killing enough of these may give credit for collecting the yeti-like Snowman normally found in El Nath instead (happened to me). These are all weird quirks, but each one of these monsters can be collected through normal means as well.
The problem is, each monster listed above does not currently appear in normal gameplay with the exact name shown in the Monster Collection, leading to suspicion that they are currently impossible to collect by any means short of using a Monsterbloom, an item so rare I'm only aware of 6 of them being available from the recent Party Punk Monster event. AlexF, further in this thread, has stated that most of these should be collectible because the monster names need not match exactly what is visible to the player to allow collection, due to the system apparently matching background hidden text strings that we wouldn't normally see instead. As an example, he states that he has collected the Magic-resistant Commanding Possibly-Evil Seal even when the visible name in the Monster Collection was off a bit, which is very hopeful. For the time being however, I must remain skeptical until I can confirm these entries myself, or have sufficient evidence from others as well. All evidence I've been able to see so far continues to support the basic monster name == monster collection name theory, as noted in the above paragraph. Even the oddest monster typo I could find in the list/game, "Mithril mutae", spelled exactly as such with 2 spaces and a lower-case M on the second word, out of formatting with all other monsters I've seen, still has the names match both in gameplay and in the Collection, and I've been able to collect it that way. Once again, further testing may confirm AlexF's claims on the nature of the system, but I will leave the list intact until otherwise noted.
Wall of Text preamble out of the way, I'll go in more depth on the trouble with each monster.
For Zakum1(sic), this entry refers to the old version of Zakum, before he received a revamp to the current version in-game. Before, Zakum had 3 distinct forms named Zakum1, Zakum2, and Zakum3. With the revamp to the boss, these have all been folded into a single enemy with one life bar, simply named "Zakum". I have read posts dating back as far as September 2016 noting this problem, and I believe that this version remains completely impossible to collect at this time.
Next, Elites with the KO and Seductive prefixes. These prefixes no longer spawn in normal gameplay, apparently having been converted/merged with "Overwhelming" and "Charming" respectively. However, it is uncertain if killing the correct elites with these prefixes will actually give a chance to collect the monster or if this remains broken. I am currently testing elite kills on Steel Xenoroid EXs and keeping track of how many of each prefix I kill for testing purposes. Further updates as I make progress.
The Magic-resistant Commanding Possibly-Evil Seal may be working at the moment. As I noted above, AlexF says he's collected this one even with the name in the collection not matching exactly (should read as "Magic Resistant Commanding Possibly-Evil Seal"). Until I or others can confirm collecting this monster right now, I will leave this one listed for now.
The Ripe Wolfruit elite is an odd case. There was a period where most elite's prefixes were displaying as ??? due to some text error. It just so happened that this monster was listed in the Collection as ??? Ripe Wolfruit, and it appears that numerous people collected this one during that time frame, because the names would therefore match exactly. Both issues have since been corrected, but the monster is now listed with a non-existent "Charismatic" prefix. This makes it uncertain what, if any, prefix will actually allow the monster to be collected. I suspect it was meant to be Charming, but so far, testing hasn't borne any results for me. Further updates in the future.
Finally, the Reindeer is an especially interesting case. Rather than having an improper name, it's actually the name of two different monsters. This gives it the opposite problem from what I stated the in the first paragraph. Rather than multiple monsters being useful for collecting a single entry, it's been reported that both entries can't be collected because killing the Reindeer found in the Lion King's Castle instead provides collection credit for the one in Mu Lung. I intend to test this on a fresh server where I haven't already collected the Mu Lung Reindeer, but if the system works as expected, this is the sort of thing that could potentially happen.
I believe that is all of the potentially impossible-to-collect monsters in-game at this time. I will continue to update this report as I gather more data. I appreciate everyone who has provided their own information and pointed me toward other issues I hadn't noticed myself. If anyone has any other problem monsters, or can confirm having collected any of the listed monsters at any time AFTER this was originally posted, it would be a huge help.