Weird.  On an MFJ return there is no option or toggle to make this occur.  Sounds like something happened when the payments came from the spouses individual account, but I have clients that do that often (hell, I do that on my MFJ return and my separate account makes payment), its never been an issue.  Im sure youve verified that the return isnt accidentally marked MFS. 

The IRS  got the money on time, I would dispute any penalties sending proof of payment along with a copy of the joint return.