Does your crate have a divider in it? If not, it could be that the crate is just big enough so that she can find a spot to go away from where she sleeps. There is really nothing you can do once you have discovered that she had an accident in the crate. What's done is done and disciplining her will do no good. All you can do is clean it up and take her outside. At 3 months old, puppies have very, very small bladders and need to be taken outside constantly. They need to go out after eating, drinking, playing, and waking up from a nap. Also, it's a good idea to pick up the water bowl at least at hour before she gets crated for the night, as well as be taken outside right before bed. If you are already doing all of these things, I would suspect a possible UTI.