When using version 2.1.2.5, I noticed that when I have a merge conflict, and use and external merge tool (Beyond Compare) to resolve it, then the behavior of SourceTree is broken. I save the merge result in Beyond Compare, and close Beyond Compare.  SourceTree closes its "Merge in progress" dialog, but the file continues to be displayed as a conflict.

I have uninstalled 2.1.2.5 and installed version 2.0.20.1, and fortunately it works properly.  I.e. after you close the external tool, the file displays as resolved.