The "goof-up" I frequently discover is that the gametype was never assigned. Now if you do this the conventional way, open UT and select a gametype and then the available maps you'd never notice this sort of thing, but I frequently double-click a (for example) CTF map and it opens up in Deathmatch, and occasionally in Domination.
Fixing this is simple, though it means I've gotta rename the map to avoid potential file conflicts:

If you double-click this CTF3 map, it opens in Domination, as it was assigned the wrong gametype:
https://unrealarchive.org/maps/unreal-t ... a0965.html
Although the map has each of the 3 flag positions duo setup with control points too.
If you double-click this CTF map, it opens in Deathmatch, as it was assigned no gametype:
https://unrealarchive.org/maps/unreal-t ... 459f3.html
Although that Appalachian-Wonderland map is a lil' bit more tricky...

...as it's setup for both CTF & DOM, it has flag placements & control points setup.
Curiously, UnrealArchive has 3 listings of that map, 2 for Deathmatch and 1 for CTF but nothing for DOM.
Possibly only I and Silver Ibex (guy who made the map) have the map setup for Domination, I renamed a copy to DOM-Appalachian-Wonderland.
Most of the older UT99 maps aren't specifically assigned a gametype, even if they're configured for it... but the issue persists as even more recently made maps don't always have the gametype assigned. Not that this is an issue for most players, as they don't launch the maps outside of UT.