First, does your org's published pricing policy say something like "Pricing subject to change without notice"?
If yes, then you are covered. For those who 'fell thru the cracks,' I would go back to them, explain the situation, profusely thank those who understand and agree, and notify those who do not that this was their last free ride.
If no, I would advise that wiggle-room wording be added as quickly as possible. Then you still have to do the same: inform your customers, profusely thank those who belly up to the payment bar; put on notice those who don't.
And, regardless of yes or no, I would also take this opportunity to have a word with staff. Policy is policy, and staff must adhere. Sounds like some did not.