3823713 - Why did Concur Travel allow me to book 2 carriers that have no agreement between them?

The issue stated is that a reservation was made in Concur Travel for 2 different carriers- one carrier (Jet Blue) on the outbound and 1st leg of the return and the other carrier (Alaska) for the 2nd leg of the return. 

In the connecting city on the return where the transfer from one carrier to another should have been easy, the traveler was asked to recheck the bags and go through security again because the first carrier Jet Blue and the 2nd carrier Alaska did not have a ticketing and baggage agreement. This caused delay in connecting to next flight. 

The question the traveler is asking if this is correct and why Concur Travel allowed traveler to book this combination.

Why did Concur Travel allow me to book 2 carriers that have no agreement between them? , KBA , CON-SRV-TRV-ADM-TVE , Travel Vendor Exclusions , Problem