The first programmer creates a public variable (GameObject, for example) in any script, then he assigns a game object to this variable in the inspector, then he makes a push, then the second programmer gets an update and there is no game object in the inspector. We have .meta files in our project, Asset Serialization mode is Force Text, also we use git and bitbucket. It happens not all the time and not with all references, only sometimes. What’s the problem and how can we fix it? Unity 5.3.3, but it also happened with prev versions.
Check out this great plugin to find all the missing refs
http://www.tallior.com/find-missing-references-unity/
also check this unity answer ( although I think it is best to try it at the start with an empty project )