My chanseys all learned toxic (TM06) from father roselia along with egg move aromatherapy as well. shuckle should still learn toxic from dustox so long as father dustox knows it.
It's not a flaw, the Pokedex only lists EGG moves, which you can only get onto a Pokemon by breeding. HOWEVER, if the father knows a TM the baby can learn, it will always be passed down.