I would agree that her two weeks is over. It is not by the amount of days that they are present, but the weeks gone by. Maybe she misunderstood your contract, and thinks that if she didn't let the third week begin, then she is still fine as he never started the third week.
Her reason for pulling is very weak. Maybe she has changed her mind about putting him in care (as 3 is old to start a new daycare, unless he came from another one), and is giving you a lame excuse. Either way, it really doesn't matter.
If you want to try and salvage the situation, maybe explain to her that her son is probably just going through a temporary "regression" of sorts due to just starting a new daycare. He is probably just a little bit sucky and needing some reassuring from his mom after being at daycare, and she is putting it to the ages of kids you have in care.

Good luck with whatever happens. I hope she honours your contract and decision. If she gives you a hard time, I would probably give back her deposit or come to a comprimise of returning one week.