It could be a player issue (though if it is it's hard to say when, if ever, a fix is found and implemented) or it could be a makemkv issue causing it. I'm leaning towards Makemkv just based on the fact that playing direct from the disc works perfectly. When Makemkv extracts the movie to the mkv container it should be just like it was on the disc. The fact that these errors occur means something is different. The fact that YOU haven't experienced them, means that it could be problems with makemkv and certain players, requiring a fix on one, or the other, or both.
Extracting the Truehd track without the atmos meta data means we can potentially play the movie with no dropouts (no atmos either, but at least retain the lossless audio for the most part). Whether the receiver is decoding the atmos or not is irrelevant. I've had the same problem on 3 different AVR/processors, 2 of which were atmos capable and 1 of which was THD only.
Just got to thinking... What would happen if you used the THD track from the bluray and remuxed it into the UHD mkv? I know there not guaranteed to be exactly the same and there may be a time alignment issue, but other than that, they're essentially the same. Just looked at the bluray disc for Incredibles 2 and it uses DTSMA. Still... Wonder what would happen if it was Muxed into the UHD track? I might give it a try just for the hell of it and see what happens. lol