They've happened quite a few times in Sins history. They're also very hard to find and fix, so if you have saves or anything else that can help the Devs fix the problem. From the "How to provide feedback" sticky.

For Multiplayer Desyncs:

If you're playing a multiplayer game and desync, make sure that:

1. That nobody is using a mod - or - that everyone is using the same mod and version.
2. That you can reproduce the issue from your last save game or autosave.

If you can reproduce the desync, please see this thread for how to help us track down the issue: https://forums.sinsofasolarempire.com/415093. Please include as much detail as you can on what appears to be causing the issue or when it occurs. If the desync is caused only with a mod, we recommend you contact the mod author.

Every game I start with a friend will desync fairly quickly, bevore we even take our first colony. Same version, no mods, etc.

Yes, 

I tested this with my friend again today, we started 3 games and we had 3 desyncs.

Will try to make him change those files, so we can track that problem down and send in files, also the desyncs only happen to us since the new update.