Yes, pellets with treats in them are very bad for them. Since she is nursing babies she should be on a good 16% protein pellet and the babies will need that type of pellet too until they are full grown. Ask local feed/farm stores what they have and try to get as high of fiber as possible. Except for Oxbow, which has lower protein, I have not seen any worth while alfalfa pellets in pet stores. Brands I've heard good things about are PenPals (I buy this for the shelter rabbits), Purina, Blue Seal, Manna Pro, and Purina High Fiber.
When the babies are weaned, the mom should be switched to a food meant for adult rabbits, preferably timothy pellets. I love Oxbow Bunny Basics/T and can't recommend it enough. Kaytee and Zupreem also make timothy pellets that should be decent and fairly easy to find in pet stores.
Nursing and growing rabbits need a lot more energy. You can free-feed them pellets as long as they still eat plenty of grass hay. If they are ignoring the hay then cut the pellets back until they eat a decent amount of it. Adult rabbits always need limited pellets. About 1/4 cup per 5 lbs weight, although some rabbits will need more or less to maintain an appropriate body weight.