I just filed the N400 forms for both my wife and I. Sent them in the same envelope and there were no issues, at least none that I know of. I used her credit card on her application and my CC on mine, both were charged the appropriate amount, so that tells me at least someone saw both applications!
As for the name change, your wife should've checked "Yes" in the section where it asks if you want to legally change your name. If you check that box and indicate what you want the last name to be, there shouldn't be any problem with that would be my guess.
Just leave those sections that do not apply to you as blank. Don't need to put N/A or NA or anything else.
Good luck with the applications.