When the Clear Hotbar option is enabled, you can't take out items from the bundle, because they use the same buttons and work at the same time. 

Steps to reproduce:

1. Go to Settings -> Controls -> Controller enable Clear Hotbar
2. create a world in creative mode and enable "bundle"
3. Put some items into the bundle
4. Choose the bundle and press the X key on the controller

Observed result:
The hotbar becomes empty and the items disappear.

Expected result:
The items are taken out.