I forgot to mention: companions (from shrines at least) and decoys (from evasion) also seem to block and absorb auto-attack projectiles (though that might be intended).

I'm not sure if this helps, but I turned off the "Basic Attack" settings in gameplay and I stopped having issues with it not correctly hitting destructibles. I don't seem to have the problem with champion monsters now, nor are evasion decoys from "Shadow Cast" rune absorbing arrows, and neither did the rat companion when I just had it.

The only information I was able to find on the setting came from this source:
https://www.reddit.com/r/Wolcen/comments/f3eh4q/what_does_the_basic_attack_setting_do/
Based on that, my guess is that when the left mouse button is held down, the basic attack isn't actively updating targets, and thus is ignoring them completely if it didn't originally know that they were there.

So yet another update:

Even with Basic Attack turned off, it is still occuring (but it does seem to happen rarely now compared to before when I had it turned on.