Disclaimer: This might not be a bug. I'm not the best breeder, and I tried to do some research after I noticed it was happening, but I didn't find anything conclusive
Anyways, I'm doing a dark monotype, and I'm trying to breed moves onto my Vullaby. I figured out that I could get roost from a pidgey, and knock off from a Farfetch'd. I bred roost on first, and then I bred on knock off. With the new Vullaby that now had the two egg moves that I wanted, I pulled Ditto out of my PC because I wasn't satisfied with the IV's of the Vullaby that I bred for, so I decided to breed a few more eggs. I grabbed 3 eggs from the day care, and decided I'd just do 3, because I didn't care too much. I hatched the first, but it wasn't that good either. It knew all of the egg moves. When I hatched the second, however, it had pretty good IV's but it only knew roost as it's egg move, and didn't have knock off. I hatched the third to see if it would have the moves, but it also only had roost. Like I said, not the best or smartest breeder, but this might be a bug too,
EDIT: Lock/delete please