If the sounds you're hearing are very variable, instable, mostly of low frequencies, and seem to vary touching TRIM knobs,
just have a look on this.
First try to *disable* completely MIC/GUITAR inputs and see if noises disappear.
If they does, there some possibility the problem is related to defective potentiometers, very well known problem.

MOTU 828 MKII have often defective MIC/GUITAR inputs causing very annoying and unpredictable noises,
even with sensitivity TRIM set to minimum.
The cause is in two potentiometers with defective terminals (not the usual wiper problem of pots).
They are IMPOSSIBLE to find in the market.
In this tutorial I will explain how to build compatible potentiometer, even on the mechanical point of view, and fit the problem spending only about 10 $ !!
 
Since it's not possible to publish a YOUTUBE link here, go in YOUTUBE and look for "MOTU 828 Bob Axx" and you'll find the tutorial.

Please be aware that all these modifications will obviously VOID THE MANUFACTURER's WARRANTY ! :)

Enjoy!