I believe the pup is confusing the rugs with pee pads, reason why she is peeing on them. If those rugs are light in color use dark ones maybe that would help distinguish pee pads from rugs.
I adopted a 2 1/2 yo male in 2013, he came with pee pads even tho he was house broken so I knew he knew what pee pads were for. I am retired and home much of the time, but there are times I have to be gone 7 hours, I always left a pad out for him. I have a dark rug runner in the kitchen in front of the sink and in the living room where there's the most traffic, dark ones at the front door and off white in front of the sofa. The times I had to be gone for 6 / 7 hours he never used the pad, he waited until I came home to go outside to potty. Then I started to smell urine!!!! The pee pad was un-used, I lift the runner in the kitchen, no stains, I lift the dark runner at the front door no stains, I lift the off white in front of the sofa

stains. I threw it out, shampooed the carpet and laid down a dark runner, that was 3 years ago, he has never peed on the dark runners. So, he was confused with the white pad and the off white runner. He may use 2 pee pads in one year, he will wait until I get home to potty outdoors if I am gone for 6 / 7 hours. Anytime I am gone that long I check every runner, and no more pee stains.
Reason I am suggesting if you're using light colored rugs, try dark ones.
Good luck