Scrolling up in a bundle works just fine, but when I scroll down with a container open, instead of scrolling through items in the bundle, it move items from the bundle into the container. I'm not sure if this is intentional but it feels quite annoying. I'm on Fabric 1.21.3.

Indeed. It is not intentional. I'll need to see how Minecraft handles bundles and how to fix this.

i think a simple solution might just be to special case bundles, so that they aren't able to be moved with the mouse wheel

you could potentially still allow moving empty bundles

I special cased bundles in e3e66e8 which fixes this issue. Unfortunately, the built-in Fabric API hook doesn't tell the mod Minecraft's scroll handling return value, so this is not a generic solution.