Happens to me also. You can CMD+ALT+TAB and Up arrow Down arrow rather than restart. You're not alone, I also find it annoying when it happens.

On Wed, 12 Oct 2016 at 21:09 Igor Kozlov <me@igorkozlov.me> wrote:
Sometimes when I'm working on a project and jump between branches TM suddenly stops scrolling to the current file when I press "Go to current file" (⌃⌘R) even though the file gets selected.
This is happening for a few months already. I usually fix this by restarting TM, but it's not the best workaround since I lose all the undo history.
Am I the only one getting this? Or I'm just the only one getting annoyed by this?

textmate mailing list