Updating Unity to 5.5.2p1 fixed the issues we were having.
We submitted a bug report to Unity a while back and here’s what we wrote:
1. What happened
We are developing a game on one windows pc and one mac pc. It’s not normal that unity crashes in this way, however when making big merges between mac and windows unity behaves very unpredictable.
2. How we can reproduce it using the example you attached
Make changes to the csproj files from unity and try to merge between windows and mac. it’s often hell.
3. this would probably not be a problem if there was a way to tell unity where to place dependencies, so we can have them directly in the project folder and therefore have relative paths to the assemblies
Unity responded with:
Thank you for submitting a bug to Unity.
This issue is already fixed in version 5.5.2p1.
If you have any further questions, feel free to contact us.