Payments Incorrectly Applied to your balance. CP60

I just received a letter saying that my payment was incorrectly applied to my balance due and removed, and now owe more because of interest and penalties. I got a notice when I made the payment that it was received, and it still says "pending" on the website.

Why would it say that it was "incorrectly applied"? What does that even mean?

This is only my second year filing since I graduated college, so I don't have any other issues where it could be misapplied.

And now I can't even get through on the phone.