Hello!
Thank you for making a Bug report.
Per the way pendulums work: When a pendulum card leaves the field it is sent the extra deck face up. In the extra deck, the effect upon destruction activates, that effect being to place themselves into the pendulum scales. This effect is optional, so you must agree to the prompt to activate it after they have been placed in the extra deck.
There is a chance that the effect is broken. I will take a look at it to confirm.
Please standby.