The beep is a timer alert. It means either the food in one zone is done cooking, or the second zone has just started its cook cycle.
Fix: Press the START/PAUSE button to acknowledge the alert and silence the beep. Check the display to see which zone's timer has ended or begun.
If that didn't work: If the beeping is continuous and unrelated to a timer ending, or if an "E" error code is displayed, unplug the unit. Wait 15 minutes, then plug it back in. If the issue continues, contact Customer Service at 1-877-646-5288.