score:2
This is simply a problem with the online check-in system of some airlines. Airlines can check if for a passport number, a valid ESTA exists. If you do not have one, online check-in may fail as they may be unwilling or unable to check your visa at the gate.
But that's not a real problem because then they will check you in at the counter at the airport instead after verifying that you have a valid visa.
Upvote:0
The airline should be able to handle travelers from VWP countries who have visas, but many airline systems seem to have been designed by people who have failed to take into account the fact that such travelers exist.
The next time you enter the US, present your passport to the passport inspector open to the page where the B-1/B-2 visa has been placed. Avoid using automated passport control if you can.
Because you plan to leave before the 90-day limit, you should not worry about any negative consequences of your having been admitted in the wrong status.