Can you actually measure the misalignment? Can you show beyond doubt that the tubes are out of line or out of square? If the frame is misaligned it will not be as strong as a properly aligned frame would be---not necessarily noticeably weaker, but it cannot transmit forces quite as well as an aligned frame.

You might need to consider legal remedies.

Also ... if you send an email and they blow you off, they win. Their thought would be, "He doesn't care, so too bad for him." if you want a properly assembled frame you will need to call, and call again, and fight it out until you get what you want.