I'm not sure what you mean by this.
If you are referring to the telephone booking fee BAEC might waive the telephone (offline) booking fee in this circumstance. The oft-stated rule for waiving the fee as explained by BA Executive Club is if a functionality is available online but is not working correctly then the telephone (offline) fee can be waived. In this case your position would be as the functionality for booking partners is available online but it is not working correctly (the connections are not showing properly) then the fee should be waived.

Of course, you could as suggested by guv1976 just book each flight individually online.