When you check quickly multiple files to stage them, most of times appears a dialog titled "Staging files" with this info:

git -c diff.mnemonicprefix=false -c core.quotepath=false add -f – my_path/my_file
fatal: Unable to create 'my_path/.git/index.lock': File exists.

If no other git process is currently running, this probably means a
git process crashed in this repository earlier. Make sure no other git
process is running and remove the file manually to continue.

Completed with errors, see above.

Pressing the close button does nothing and the dialog remains in front. I can't keep working and I must restart source tree.