2012 2.4 engine manual transmission hearing weird noises

This tranny was replaced 5 years ago and is under warranty it wasn't new it was used, had it in the shop less than a month ago front axle and CV boot broke so that was replaced, oil change done still hearing a tapping in the engine area, Jeep back at the shop they're thinking it could be bearings so they called the Savage Yard who warrantied the tranny and they're saying it's not the tranny they're thinking it's a rear differential and I didn't know driving down the road when you accelerate you would hear like a tapping or a pinging noise if it was a rear differential. So now a transmission specialist has to go to my shop to decipher if it's their transmission that's under warranty or if it's a rear differential which my extended warranty will cover. Has anyone ever heard of a rear differential making a tapping or pinging noise when accelerating and making it hard to shift gears. This 2012 only has 50,000 miles on it