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I thought being pregnant was the usual state for female mollies. They can have 5 or 6 batches from 1 breeding. They store the sperm. On most colors, you can see the gravid spot on the tummy. Blacks and marbrls you can't see. Welcome to the world of live bearers. Better start shopping for another tank
It sounds like you may be having a new family of mollies in your tank! Be prepared because I had two females that had babies almost every day for a week. We had so many little guys that we had to keep sending them back to the lfs.
I think that would be best, then when she gives birth you can move her back. I'm not sure if thats the right thing to do, but it's what I would do. I belive they give birth more then once because they store sperm, so make sure you ask around.