Shift-clicking items into the crate works as expected (ie. stops when the item limit is reached). But items can then be manually moved into the crate, causing it to go over the item limit. I don't know if that's intended behaviour or not. I replicated it in both creative and survival mode.

Steps to recreate:

1. Place a crate.
2. Fill it with 10 stacks of cobble (these can be shift-clicked into it).
3. Place even more stacks of cobble inside by manually dragging the stacks into the inventory.

Log: latest.log