If you have an item in a container that is stacked to 127, then adding or removing an item from that container by using ctrl + enter, the item will go down to 64.

NBT Editor shouldn't make assumptions about the max stack size being 64, as it can actually be up to 127 (though the game itself handles this weirdly)

I did a quick search on Github just now, and I don't see any relevant references to getMaxCount() or 64, so I'm guessing this has to do with Minecraft code that I reference. Do other types of edits also cause issues (nbt editor / item factories)?
I'm assuming by Ctrl+Enter you meant Ctrl+Click or Ctrl+Space, since I don't believe there is a Ctrl+Enter keybind.

Can you also check if an item with a lower max value (like enderpearls) is limited to 64 or 16? Thanks.

The main reason 127 is technically possible is that item counts are normally stored as a signed byte (-128 to 127). However, the game's code has been designed with 64 being the final limit in mind, so glitches would be expected. That said, as a mod focused on making interesting items, I would like to do my best at supporting quirky features like items stacked to 127.

Any items that dont normally stack to 64 (like enderpearls) do not break. If it is stacked to 127, when the container is edited it is brought down to 64.