This can depend on a few factors. For example, if you started the update from the launcher while the maintenance was ongoing.
Many people find it easier to patch via the GameLauncher.exe file located at C:\Nexon\Library\maplestory\appdata
I would recommend performing a full restart (on Windows 8 and Windows 10, you must do this manually via Command Prompt run as an administrator using the command "shutdown /s /t 0", or you must disable Fast Startup in the settings menu) to clear any troubles, followed by updating via the game launcher. When you're not playing, open the launcher and select the gear icon, then select "repair installation". Let it run overnight or while you're out and it should go back to normal.
Windows 8/10 full shutdown instructions: