git pull bugs when error occurs

When you run the git pull command on linux, you may come across a bugs that if one file or directory has permission problem.  Once the permission (or any access I/O) problem comes out, the files' modification date before the error may changed to current!?

Then, what happen?  Once you fixed the access or I/O problem and run git pull again, thousands of conflict come out because of the file date changed. 

This problem is impossible to recover.  Good practise is BACKUP, always.  Make a good ignore list.  Remind yourself to fallback the write permission of the files and directories before.