SteveC
Doing the best imitation of myself
Sigh.Example of monsters that have incorrect attack bonuses for their CR?
I suspect you are confused about how monster proficiency bonus is determined. It's based on CR, not HD.
If your DM introduced too many magical sources of AC, I can see that restricting stacking might be useful. This is basically a fix for a problem your DM created, but whatever works.

Many creatures have a lot of Hit Dice because they end up being big bags of hit points. I have no issue with treating them exactly like characters and basing their proficiency bonus accordingly. The fact that this makes large creatures slightly stronger is a feature to me.
I have a similar reaction to the magic items comment. If D&D is about killing things and taking their stuff, we want to make sure they have some stuff to take. Our DM uses the treasure generation rules from the DMG, so it's all been left up to the dice.
It's, interesting, I guess is the right term, to think of D&D as being unbalanced once you introduce basic magic items into it. That in itself is a problem, since having magic items be a part of the game is as old as the game itself.
I'm looking for ideas on how to deal with the cases where ACs and hit bonuses are outside the normal ranges for bounded accuracy, which I believe to be an issue. Perhaps you don't find it so, and if that's the case, enjoy your game.