Desyncs can be tricky to pinpoint at times. Sometimes it is the map's fault. Sometimes it is not. Sometimes it is not even map related. For starters, I would suggest you restart your Warcraft 3 before joining maps you seem to desync from because other maps you played earlier may be causing the problem. These earlier maps could optimized in a way that will poison the game cache, and cause desyncs in other maps you play later.
If you continue to run into desync issues with Gem even when restarting before you play the map, please make a topic in the
Gem TD+ forum. Be sure to include replay(s) and any other information that might be helpful (look at how to report a bug).