When using the bundled feature, if the item that is getting checked out has a 952$3, the check-in will not be successful.  This main item can not have this field, although this field is helpful for staff to know it is a bundle and has items included. 

Step 1.
Create a bundle of items
Step 2. 
The 'main' item in which will be checked out to the patron - make sure it has a 952$3 with text.
Step 3
Check out the 'main' item that has the items attached to it. See the materials specified text appear at checkout.
Step 4
Checkin in the 'main' item and the subsequent items. 
Step 5
See that all items are verified
Step 6
Koha will bring the staff member back to the screen to do the check-in.
Step 7
Go to the 'main' item and see the bundle is still checked out to the patron.

Removing the materials specified from the main item, and the check-in will then be successful and be removed from the patron's account.