Hello @VanIsle19 ,
Every time you use a credit against an outstanding bill in the bill payments screen, QB always makes a $0.00 entry with the following in the memo field:
QuickBooks generated zero amount transaction for bill payment stub
Even though it is a $0.00 payment and credits have been used to "pay" the bill, whatever bank account you have showing in your pay bills screen at the time you record the "credit" payment is where this transaction will post to. I purposely post these to a Bank Account I created called "Internal Clearing", just so my regular bank account isn't cluttered up with $0.00 entries. You just need to find those $0.00 bill payments, delete it(them), and then your credits will be available once more to apply as you choose.
You can do an advanced search with some of the words in the above phrase in the memo field and you should be able to locate them fairly easily.
Good luck!