Set up everything so that it Makes Sense why it's there.
In other words, don't have a mindflayer sitting in a cave, and 20 feet down a tunnel, sitting in another cave, is an ettin.
If this was a real case, the Illithid would be Controlling that Ettin.
However, if you can come up with some clever ways on how monsters can co-exist, go for it. Like a nest of kobolds who train Stirges to protect them from the Chuul that lurks in the water caves under them (Chuuls have no defense against stirges, since their AC is pure Nat, and stirges ignore that).
Things with ecological reasoning are always good. Like, little rivers that have fish, animals, edible lichen on the walls (Glowing lichen is awesome

). That way your monsters have something to Eat, and live, and so forth.
What's the underground thing like? Natural caves? A constructed, deserted fortress? More details will help.
