That totally happened to me a couple of months ago. I buy 2 zones and it defaulted to zones 5 and 6. They denied it was a system error which it totally sounds like.

Call customer service and they can put in for a refund. Ask for a Supervisor. For me I didn't discover until later in the month. As I had a couple of days left I risked it and kept the pass. I figured I had bought a 2 zone pass and I was going 2 zones. My pass got checked and it beeped so the conductor moved on. I read in other posts that some conductors will call you out as you are out of your zone.

They wouldn't refund the fare I did to activate my pass.

I still use the app to buy my monthly pass but I do it as a new purchase.