I was tooling around yesterday on a WMA. I was on a "road" and nearly got run over by a couple of locals on 4-wheelers. I assume they are local because I was on a dead end road, coming out, and never saw a trailer.
As a general rule, no they cannot be on a WMA. The one exception is during big game hunts when they may be operated on open roads. See page 16, column 2, Vehicles section in the current regulations. In other words, they may be used in the same places you could drive your truck, NO OFF ROAD USE. Please contact the WMA manager of the WMA you were on and give him a description of the ATVs you saw and of the operators and the location. It is likely that the manager is aware of the situation and is trying to catch them anyway but information is always useful. ATVs are kind of hard to catch up with at times, you can usually catch the slow ones or the dumb ones but you can't get all of them all of the time.