I'm not saying that this is the cause but it does happen to me a lot.
I have a habit of looking at shots from a lot of angles and from time to time when I do I end up with a reverse angle, which of course reverses the wind. I click back with the shot in my head only to hit and realize that I have completely botched the shot because I factored in the wind backwards.
I might be the only idiot that does this, I'm guilty of it on putts from time to time as well but while I'm not defending the glitches in WGT, I do know that I make plenty of my own.