What are .rej files which are created during merge

.rej files are rejected files (usually hunks patches but not only).

When ever you get those files after merge you will manually have to edit them, fix them and then apply them back.

You can read here some more about it and what is it

.rej file

diff a.txt    (rejected hunks)
....

Fix it manually and then apply the .rej files like a regular patch.

manually merge the change from *.rej into the required file and remove the *.rej file.

Another very usefully article addressing this can be found here.