I have one female molly who is very skinny, she is fed bloodworm twice a week and flake food. Other than that she appears healthy?

could she possibly have some sort of internal infection or worms?

usually losing weight if eating well there is some underlying problem... I'd keep a close eye on her.

Is there also a chance she's not getting enough of the food, maybe being pushed away by others?

No ive watched her she is getting decent amount, shes been like this since i got her. That was over 5 mouths ago.

maybe it's just her gene pool and she'll just always be skinny.

Well shes the only female no to have fry, so maybe sterile to lol. Ive got a dude.