If so, all you need to do is to remove the bad squares and replace them. I do hope that you over estimated the floor job back then and saved some extra squares?
To do this, get a sharp chissel and gouge a hole in the middle of the square, then carefull work out to the border. Do not gouge the neighbor or you will be replacing it also. When removed, clean out the debris and old mastic, then lay the new tile in the hole being sure to follow the position of the new tile.
This is it. Now if you have sheet vinyl, let me know and I will tell you how to repair that