If the bank previously has an online form that did not allow the designation, but the online form now does have the designation, that could potentially allow an argument that the interface was ambiguous. On the other hand, if there was a FAQ or instructions on the web site that specifically said "contributions for prior year can only be made by check and you must use the specific form" then that would allow the bank to argue that the customer didn't follow the clear and unambiguous rules.
Bottom line, if the bank won't recharacterize the contribution (no matter what their argument is) the taxpayer either has to sue the bank, or amend their tax return. I doubt that suing the bank is productive or cost-effective.
