Is there a problem if we have intent to apply for “joint credit” on an application, but the loan ends up being written as a loan with a co-signer and not co-borrowers?

Unless you have documentation as to why the joint applicants decided to change their minds in the file - yes.

I don't think this would be a matter of the applicants changing their mind, but more of a situation where an ordinary folks, don't have an option to mark "co-signer" on an application and use "joint credit" instead, knowing this is their intent...to co-sign.