Amazon Games created a forum post about Addressing Desync Issues
The short version is this; It happens when the data from the server and client are mismatched. The Heart of Madness patch increases the frequency in which the server sends data to the clients, so this should help with the problem. However, it may cause more players to freeze up in wars, so keep an eye out on it. More fixes to address the problem will come, but it will take time since one change can't fix everything. Keep reporting problems on the forums.