Did the IRS provide a contact number on the ITIN rejection notice? I would call if you can and let them know about the error and ask about the other dependent. It is possible that the applications were separated from the tax return for 2 but not the 3rd and they should be able to offer some additional advice regarding how to finalize with the forms you already submitted.
They should also be able to locate and tie together the information from scanned images. It sounds like an error on their part, honestly, which hopefully you can fix with a phone call. If there is no phone number you can write to them, but there should be a number for inquiries on the letter (which will direct you to the office best able to assist you.)
@santhoz
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