Git for Windows 2.12.2 has a regression in git status which causes editing files to fail The regression has been fixed, and the fix will be included in Git for Windows 2.12.3, when that is released. There may also be a Git 2.12.2 (2) release before then which includes the fix.
There is nothing Bitbucket Server can do to fix or workaround this issue, which triggers a segmentation fault in some repositories. File editing is the only feature known to be affected, but it's also possible the git add operations performed as part of handling pull request merge conflicts may also fail (based on this report).
For the moment, the best solution is to downgrade to Git for Windows 2.12.1, the release before the regressions were introduced.