Complaint sub-issue: Billing problem

I have an auto loan with PNC Bank that is seriously hurting my credit score. Numerous late payment complaints have shown up on my credit score from them due to late payments and the payments I am making over the phone and online are not going through.

Originally I started out trying to make online payments, but even though they looked like they were scheduled properly I quickly found out from the late notices two months in a row that it wasn't working. I should have complained then, but each time I called in and made the payment over the phone and was told, " Oh don't worry, if you pay right now with me it won't affect your credit score. ''  Eventually I got into the habit of simply calling in and paying over the phone and that was working fine, but when I went to try and get a loan to buy my house I found that those late payments were indeed showing up on my credit report despite me paying them in full immediately upon discovering their computer error. 

Now, after having paid over the phone for months, I get a notice of default saying that I am overdue. I called them to find out what happened and how I could possibly be late today ( XX/XX/2018 ) and they told me that they did have a record of my call on XX/XX/XXXX and the payment I made, but that it was rejected due to insufficient funds. 

I looked through my bank statement for both XXXX and XXXX and at NO TIME during the month did my checking account even come close to being too low on funds for the {$540.00} payment ( lowest it dipped was just over {$2000.00} ). She told me I would need to fax in a copy of my bank statement to resolve things to prove it was a glitch on their end.

Then, when I tried to make the payment today she said, " Oh I think I see what happened, looks like your account is missing a one there at the beginning in our file '' after I read her the account number off my check. But she couldn't explain how that number was missing when all my previous calls had payments go through without issue using that number in their system ( the previous phone calls PNC had used the checking account they had on file for me and I never had to read any account info to them, how did that number suddenly change? ). Nor could she explain how an incorrect account number would have accounted for an insufficient funds bounceback to them. 

I never got any notice from my bank for the charge being rejected, the statement doesn't show anything from PNC bank when I called. I have a confirmation that was e-mailed to me after the payment attempt was made and no other correspondence after that part from anyone until the notice of default I got this week. I'm sure that when I go check my credit report there will be ANOTHER late payment notice on there, and I want them all removed. 

I just want to pay them the money I owe and not have to think about it. My last auto loan I set up autopay online in 15 seconds and never once thought about making a car payment. With PNC it is total stress every month. It shouldn't be this hard to pay someone what I owe when I have the funds readily available at all times, and they won't accept any kind of advance payments or anything.