This is an indication that she is bored with her situation. There are some things you can try now or soon, a combination of them is often necessary. If you can pinpoint whether this is shortly after putting her in or if it is before you return to let her out might help in trying to eliminate it. Be sure she has plenty of activity prior to retiring, and include a couple indestructible toys such as Starmark Everlasting Treat, Kong Quest or Traxx, Nylabone Romp n Chomp or processed bones or antlers (Blue Buffalo). Using spray chew deterrents is helpful for some pups as long as it does not discourage use of the pad for elimination. Once she is using the pad well for elimination you can add a collapsable play pen to enlarge her area or place the open crate in a small room such as a laundry or bathroom to give her another place to go thereby reducing boredom. Many times it is best to have a second tray and pad in the pen to make it easier to maintain the pad training idea.
The most reliable solution is a second puppy but sometimes this is not practical.