I've processed lots of sources with 5.1 audio that have "interesting" issues of various types. My favorite is when the LFE channel has a full range signal instead of a low pass filtered one. When that data is down mixed by what ever chip is doing it, there's way more data in the mix resulting in not what one would hope. These are studio provided sources that have been outsourced to 3rd parties for various reasons, but the LFE is often the red headed step child of audio data.
Idk why they have to make it so weird. My 2.1 setup just has the sub get the full signal and the built in filter takes care of it. Id been reading about how 'perfect' the atmos to stereo conversion is... what an odd issue to run into to throw a wrench in that(or just use it as a consumer). I guess theatres really need that LFE channel.