Deductions & credits

Something you said may be the key to your issue ... you said you got a NEW SS# for the child so if you filed the return after the filing deadline using a SS# that was not issued before the deadline then you are not entitiled to any CTC or EIC on the return which may be what was disallowed ... so when you talk to an IRS  agent make sure to ask about the timing on the issued SS#.  The TT program would allow the credits but  the IRS would not  and since you cannot use their old SS# once a new one has been issued you may be out of luck.