Because they are losing. and the best time to hack so it desyncs is when they are about to lose.
This is sadly often the case. Again I'll add that desyncs can be induced (to cheat), but can occur without someone pulling a fast one because of connection issues.
Even though some believe the error is related to total flag control, I don't, in any way, believe this to be the case. If I had any say in the matter, I'd rather Sorian not be investigating this supposed flag control bug as I don't think it will yield any results. I looked into it thinking perhaps it might exist and be related to different language versions of the game, but that does not appear to be the case either.
Also, I'd think we might be better off with this http://forums.demigodthegame.com/364809 being looked into and fixed.