Actually, this does occur, to an extent. There's not really a whole lot that can be done about it; wads don't exactly have much security on them. For example, while joining random servers today, I somehow picked up 3 different Amy character wads. One still uses the 1.09.4 pallete (AmyRE.wad), one has Amy with a slow thok and spindash (Amy.wad), and the last one has nospinjump, Amy holding her hammer out beside herself while she runs, and a double jump ability (AmyRose.wad).
Perhaps one of the most frustrating things about all of this (to me, anyways) is that none of these wads are in the Releases forums. We're trying to build a centralized location for people to get all the wads they need to play SRB2, but it won't work unless people use it!