I would almost have to say that something is off with the case....as I think the hole locations on the MB should be very repeatable.
That being said....you don't have to use ALL the mounts. You just have to use enough to support the board properly.
Also be aware that sometimes one or more of the mounts acts as a ground. You will see conductive trace material around the hole if this is the case. Those should be mounted with a screw.
Also, you can carefully file the hole larger AS LONG AS YOU DON'T HIT ANYTHING IMPORTANT.