I found that some prefebs containing SkeletonAnimations in my project will keep changing by itself under unknown circumstances. Those prefabs has has been there and I didn't modify them for ages. They just occasionally get dirty and I spot them when using git.
From Git client, what I general see is something like this:
The fileID field sometime change from value to 0 and sometime from zero to value.
While viewing from inspector, it does have material linked in the field instead of 0 (null).
Considering I don't see any issue whether the fileID has value or 0. I believe the SA component will always maintain the field value before use. May be it does not set it dirty in editor when value actually get changed in edit mode causing the inconsistency between the view and the saved file?
This issue has been happening for a very long time. It does not really have any impact in game but having prefabs marked dirty by itself from time to time is a little annoying when they show up in gits commit.
(using Unity 4.0 runtime)