Is there an auto-trash feature that I'm missing?

eg. if I pick up a chest full of items, and my personal inventory can't hold it, it just drops it all over.

There is not - it's up to you to know what you want to destroy or keep. Why do you have real chests full of real items? And why are you manually mining them? This isn't a problem with the provided infinity chests or by bulk deconstructing via planners.

Yes using the infinity chests.

Say I load a cargo wagon with the wrong resource and I want to remove said wagon. Am I removing it wrong?

If you're talking about individually removing a single thing - no, mining it is the most direct and quickest approach, but that puts it and its contents in your inventory, like it would outside of the Sandbox. If you deconstruct it instead, you aren't the person removing it, so its contents do not end up in your inventory.

Ok, I never used the deconstruct option. I'll check for it when I get home thanks!