The one area that I have this happen to me ALL the time, is when I hearth/recall x 5. Oddly enough only my main desyncs, he still thinks a couple of the guys are wherever we hearthed from, but the clones all see each other and the main fine. I fixed this by using my hearth/recall button, then after 5s i move my main slightly, then hit the button again, so he hearths 5s after everyone else - this gives him time to see their updated location before he then hearths. The problem was stemming from him moving at the same time as them, and losing sync.

It only happens when I'm hearthing on the same zone (outland to outland, azeroth to azeroth, etc), If I go across zones it doesn't have the issue.