Puppies pee while playing, especially at that age, so her peeing 40 minutes after she's been out while playing doesn't sound unusual to me. At 3 months they still haven't connected that the pressure they feel means they have to pee (some do, some don't)
Rules of thumb for potty breaks:
After any nap
After eating and drinking
While playing or any physical activity
Does she eat wet or dry food? Wet food has a LOT of water in it so if she's not drinking much it could be because she's getting her water from her food.
Now, all that said, it could be submissive peeing. Does she do the squatty peeing thing when she's excited and platying? Or is it just random peeing? If its random and she pees when she's not excited or receiving any attention, then she could very well have a bladder infection. I've learned to get a second opinion because vets often assume there's no problem so they tell you there isn't one instead of running tests.
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