Yeah, this one's common. You've activated the Smart Finish feature. It's syncing the cook times so both baskets finish together.
When you press the SMART FINISH button and start cooking, the zone with the longer cook time begins first. The other zone displays "Hold." The unit will beep and activate that second zone automatically when both zones have the same amount of time remaining. It's working as intended—just wait for the sync.
IF THAT DIDN'T WORK: If you don't want them to sync, you're not required to use Smart Finish. You can run each zone independently. To pause a single zone while both are running, select the zone number (1 or 2), then press the START/PAUSE button. Press it again to resume.
HEADS UP: You can stop one zone early if that food is done. Select that zone, press START/PAUSE to pause it, then use the down TIME arrow to set the time to zero. Press START/PAUSE again. "End" will show for that zone, and cooking continues in the other.