Well, I am testing a lot of pendulum decks (simply all possible duo's), and I have only encountered this bug once, after using at least 9 times the remove all button, and setting up a new deck.
I also went to the bazaar and back, but that didn't help. However, using the deckcode to manually add more pendulum did work.
1. Add some pendulums
2. Click the import/export button
3. Copy the code of the pendulums and past it some times, until you have the number you need.
4. Click import
*Note, I my case it where unupped darkness pendula.