I recently signed up for FF miles and emailed the airline to add my future trip to the FF account.

Names are:
John Smith
John Smith Jr

Smith Jr is the last name (I filled out the FF account according to how my son's passport is, with Jr being in the Family/Last Name)

They were unable to add the flight to my son's account because they said the name was a mismatch.

Up until this time, I was using the website the travel agency sent me to which showed my ticket information, of which, had my son's name listed correctly (John Smith Jr).

But I checked the actual airlines (both airlines) and it shows the name:
Johnjr Smith

While, I don't care about the FF miles as much, I am wondering if it will affect the actual flight and checkin.