I am close to a solution. Actually, I found a solution already.
- Go to the directory, either frappe-bench/apps/erpnext or frappe-bench/apps/frappe
- Check the list of the untracked files. There might be files, which do or don't belong there.
git add --all to track those files
- It should run successfully, if not, start over with 1. and repeat for the other directory
On this point you're already done, but you may want to apply your changes, which you stashed. So continue with 8. if you stashed things, which you consider important.
8 . While you're still in the folder, either frappe-bench/apps/erpnext or frappe-bench/apps/frappe type
git stash apply
Your changes will be applied again, but on the next run, you will run into the same issue like you had before.
So 1. - 7. was the solution we were looking for.
Maybe someone can tell, why "print formats" and "support/web forms" are breaking bench update. These are my files: