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It sounds like the service center issued your spouse‘s ITIN and then process the tax return without issuing the dependent ITIN’s. Is there a contact phone number or address to write a letter in the letters that they sent you?  I’m not sure how to fix this problem considering that most IRS phone numbers are either not operating or overcrowded due to the coronavirus pandemic. I guess I would try calling the IRS service center for a TIN applications. Or, see if there is an IRS service center located near you that you can visit in person.