Technically you'd maybe still come across this (unless you enable the option to force transcoding all videos).
I just tried this with a MOV file created on my iPhone and it worked as I expect (it was rejected because it wasn't encoded with H.264).
So having a file to test with would be ideal to rule out any issues with our detection. However, it might just be as simple as being a corrupted source video and the video player being slightly overzealous.