Is this likely to appear on my credit report, and can I dispute this
even after agreeing to pay the amount I owed, plus an additional fee
to the collector?
It won't appear in your credit report because you readily made (or that's what I gather from your inquiry) the payment they requested. You might get within the next few days a letter from the collections agency reflecting your payment, including also an unwarranted/moot statement about what would occur to your credit score if you default (I consider it unwarranted because agency itself has acknowledged the payment).
As for the second part of your question, my conjecture is that you are entitled to a reimbursement if you are able to prove that you were up-to-date in your payments.
I think I experienced something similar to what you describe: In 2012, I canceled AT&T, made the early termination fee AT&T determined, and then an additional "adjustment" fee from overseas. On both occasions, AT&T assured me that I was up-to-date. But once back in the US a collections agency contacted me regarding a termination fee with AT&T, so I made yet another payment (around $40) with the scare that otherwise my credit score would be affected. In hindsight, I should have retrieved my receipts and pursued a reimbursement.
If I were in that position again, I would argue that by readily making the payment I sought to avoid hurting my credit score and instantly relied on the agency's representation that there was an outstanding amount. In other words, that I acted under a [mild] scenario of hardship.
If you decide to pursue a reimbursement, start by approaching the creditor/agency. If they deny your request, then go to Small Claims court.