If you aren't creating the MKV or MP4 yourself, then you truly have no idea of the resolution, bitrate, or CODEC (for MKVs) which was used. All of these things affect compatibility within a player.
If you are doing all of the encodes yourself, then there must be something within the file which is getting messed up. I know that I had an external BD drive I was creating my rips from and I had a number of discs which did not rip properly. I recently switched to a better internal BD drive and all of my rips have been flawless.
So, doing it yourself is really critical to get the best quality.