Permission denied errors on random files during branch checkout
I don't know if you're using sublime text, but when I got the permission denied problem, I noticed there was a license notice popup; that tries to get you to donate to sublimetext3 every once in a while.
Once I closed that popup and ran the commands again, the denied permission errors went away and everything worked fine.
I extrapolate that other editors with popup notices may cause this issue.
Rebooting, as bugged87 mentioned, would certainly get rid of any popups or notifications.
The same happened with me a time ago and I've closed my VScode, typed git checkout and it worked!