It is possible that Square refuses to store a credit card's details after successfully processing a payment with that card.
In Square words:
It may be that the card itself is simply not able to be stored as card on file, which means it will be ok to take a payment but can't be stored. Some reasons may be an unsupported card type, limitation from the issuing bank, risk rules, etc.
Another cause may be that the seller's account has been adding cards too quickly or have triggered a rule that is used to prevent abuse.
When this occurs, Bookeo can only report the error. The payment however would have been processed successfully.