BYOND(355.914) ERROR: maximum number of lists exceeded (65535)!

What would cause BYOND to give me this problem? I clearly don't have 65535 lists in the whole program.

Well, clearly you do because you wouldn't be getting the error message otherwise. ;P The error is common for people who initialize lists in turfs, since there tend to be a large amount of them. We won't know what the problem has specifically come from unless we know in what situation the error pops up. Does it occur when the game starts up? When you use a certain command?
Don't worry about the message. BYOND is obviously giving you fake error message in an attempt to impede your progress. We're all sure you don't have that many lists in your program.

P.S.: Code is useful.
It may not be that many in the beginning but somehow you are causing the numbers to keep piling up (eg: defining a instantilized list for a /turf and other common objects causing it to be used up more quickly).

This is a nice article of how to improve your game.
In response to Unknown Person
In turfs? [checks code]

Whoops. [Removes frivolous map levels to lower number of turfs] Stopped. Fixed. Thanks.