Originally Posted by malmostoso

Could you share what airlines we're talking about here and on what routing? Many airlines have incompatible IT systems so it's normal to have different PNRs in the same reservation, in order to retrieve the booking on the systems of all the airlines involved.

Basically what's important is that you have one and only one e-ticket number. If you have more than one, then you can start worrying.

Originally Posted by Often1

PNR's are unimportant. What is important is the number of tickets.

However, nobody here can answer your question without exact details. What carriers, what route and are you on one or two tickets (ignore PNR's).