Getting a fatal error in git for multiple stage entries

Using Git version 2.2.0 with unity game engine on OS X, and wanted to commit my code. I added everything and did not get an error message. then commit -m , and got this error message:

fatal: multiple stage entries for merged file 'Assets/Prefabs/Resources' 

Not noticing it I pushed, that didn’t give an error message, in fact said Everything up-to-date So I checked bitbucket (where the repo is held) and it didn’t show my commit. so I checked my local log and that also does not show my commit.

I’ve looked into google for an answer… and nothing. what is this error? and how can I fix it?