No worries.  This is quite common.  I wish there was a magic cure such as just simple crating or whatnot to potty train puppies, but it's not always that easy.  Make sure to take puppy outside a LOT (at least every two hours) and use immediate praise and/or yummy treats as soon as puppy goes potty in the right place.  Make sure the treats are small enough so they don't fill the pup up, but they also have to be yummy enough to "count" as a reward for your pup.  Most pet stores sell tiny training treats.  Here are some options...

Raising a puppy is not easy so I commend you for taking the plunge into puppyhood!  Keep remembering... she's ONLY 12 weeks old... some pups don't get it for many many more months.  With a little time and patience I'm sure she'll start to learn.  Good luck!