Funny Fifteen Cents
So, I'm going along, reconciling my accounts, when I notice that one of the bills I put on my credit card was 15 cents lower than normal. I had already paid the balance of this card when that transaction was pending. Therefore, once everything cleared, my credit card had a positive balance of 15 cents. I don't use this card much, so there was only one other transaction on it, for $25, in a fully funded category.
The card balance said $24.85 was due. This makes sense.
YNAB said that there was $24.70 available for the payment, with $.15 in TBB. This does not make sense.
I ended up budgeting that $.15 directly to the credit card, as both categories of transactions were still fully funded.
But why did this happen? It makes no sense.
The real question is why are you paying so much on your credit card? They haven't invoiced you yet for those charges. Just pay the statement balance on or slightly before the due date and this will never be an issue because all charges will have been cleared and reconciled at least 3 weeks earlier than when the payment takes place.
Everything you described is the way YNAB is supposed to work, but it's confusing. You both overpaid your card and took the balance positive at the same time. The result of this is: the positive balance appears in TBB, but the Available amount in the credit card payment category is either negative (red) or too low to pay in full. The solution is simply to move the 15 cents from TBB to the card payment category.
Why do I say you overpaid your card? Because you charged $25 and then paid $25, but when the $25 charge was reduced to $24.85, YNAB moved the 15 cents back to the category it came from. So now you've budgeted $24.85 for the credit card payment but sent $25. In YNAB-land, that's overspending and has to be manually corrected.
Paying the statement balance as nolesrule suggests is a good idea, but it won't prevent this from happening again in the future if, e.g., you have a charge reversed.