In the pack, the max stacks of sizes are set to 128 and 256 for different items/blocks. With Bundles configured to hold up to 128 items, if a single stack of 128 or more items is right-clicked to add to the bundle (either of both input methods), the stack becomes unretrievable and deleted, still making the bundle full and unusable.
Stack size is increased using StackUp!

clicking a 256 stack:

after clicking:

Fixed in this commit