It's a heat buildup issue. The outer jacket of NM cable is there to protect the internal conductors from damage. Conduit's purpose is to protect the conductors from damage. Having both is redundant. A conductor's current rating is based on its ability to shed sufficient heat to prevent damage to its insulation at that current rating. When you have NM in conduit you complicate the current rating calculation. It's like wrapping someone in more and more blankets. It may protect them from bumps and bruises, but eventually they die from heat stroke.
Consider a piece of 12ga wire. It's rated for 20amps. The resistance of 12ga wire is 1.588 milliohms per foot. At 20amps, a 12ga piece of wire needs to shed .635 watts per foot. That heat has to be radiated away. If it's allowed to build up, the conductor's insulation could be damaged.
Best practice is never to run NM inside conduit. Even if you work out the current load de-rating and verify that it's safe, you don't know what the next guy may shove into that conduit. Plus, on anything less than short runs, it's next to impossible to pull solid conductor NM through conduit, when you could pull individual conductors of stranded THHN/THWN with far less effort.