Well, are they very, very small with a tanish color around them? If so, those could possibly be eggs that are developing. That doesn't mean they're fertile though. If you've had her for 3 months, even if she was a new born when you got her, she is mature enough to have babies. I read that they can reproduce as early as 5 weeks old.
But if the spots aren't as I described, then they are probably just markings!
Hope this helps
EDIT: They are definitely coloring... I just re-read your post. I misunderstood it. Sorry

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And for when she does get pregnant (notice I said when), you don't need to separate her until the gravid is pitch black and her stomach is square. She will be lethargic, also. Then you need to separate her. If she doesn't give birth w/in 24 hrs, heat the water a little bit more. Put tons of plants for babies to hide in, and then remove her when she is done. After 5 more weeks she will give birth again. She can give birth up to 5-6 times after 1 single mating. They can store sperm.
Sorry if i told you stuff you already new, just wanted to cover everything!
