When the bundle has more than twice the amount of items than it can typically hold inside of it, it will delete items from the bundle when taking them out.

Note that this only occurs when the bundle is in the mouse cursor, and you right-click with the bundle over an empty inventory slot.

Its also worth pointing out that items aren't taken out of the bundle by their slots, but rather by one full stack of the item at a time, which could be the bug instead. (MC-206962)

Steps to reproduce:
1. Run

/give @s minecraft:bundle{Items:[{id:"minecraft:stone_sword",Count:5b}]}

2. Right-click an empty inventory slot with the bundle
3. Notice how one sword came out of the bundle, one sword stayed in the bundle, and the rest were deleted