Most likely it is just being awake that is causing her to need to go. We're all like that - no need to empty the bladder while we're sleeping, but once awake, that's the first thing on the list
And that's quite normal - the bodily functions (urine production included) of all mammals slow down during deep sleep.
I'd just give her some time. Around 15 weeks is when most pups start to manage to sleep right through the night on their own. Since she's just having to get used to sleeping on her own now, instead of in bed with you, that's most likely why she's not sleeping right through. So just take her out when she needs to go, and chances are, in a couple of weeks she'll be sleeping through the night again (and in a big hurry first thing in the morning LOL).