This happens from time to time even if you do everything correctly ... so simply respond as directed ASAP so the return can continue to be processed.
** another possibility ... all the W-2 forms may not have gotten to the IRS from the ITIN office so they are missing or as mentioned above they came lose and one went missing. Also note that mailed in returns need to be entered into the system by humans and maybe they missed keying in the missing form. When dealing with people & paper errors happen which is why efiling returns (when possible) is highly recommended.
