When resolving a conflict in a local git repository using an External Tool after quitting the tool the modified file is sometimes not noticed by SourceTree and the file is still marked as conflicting. To resolve the conflict on average 3 times before the modified file is noticed and the conflict resolved.
Tried FileMerge and P4Merge as external tools.
Using El Capitan (10.11.1 (15B42)) and the latest versions of SourceTree (2.0.5.5), P4Merge (P4Merge/MACOSX107X86_64/2015.1/1233444) and FileMerge (2.8 (3005))