When I click to get a single item, it gives me two in quick succession. When I click to get a full stack, it gives me two stacks in quick succession. This makes me think these are related.

This happens to me all the time. It's really annoying when I just need one of a thing and I get two. What I've figured out is it doesn't happen when you do a really quick click. If you hold the mouse button too long, then it gives two items. I think it treats the click and the holding of the click as two separate requests? I'm no expert, but it feels very fixable, and I really hope it is fixed soon.
(I'm using version 1.12.2-5.3.8)

I can confirm. This happens for me only at first click. Repeating next clicks give expected item count.

I have experienced the same thing before. It just happens occasionally.

Looks like I don't know how github works.

Anyway, I think I've figured out that it only happens when you click from the same hand that the items will be deposited into. For example, if my entire hotbar is empty, but I'm selecting the 3rd box, it deposits only one item into the 1st box as normal. But if I select the 1st box, then it causes the double output.