My guess... and this is a stab in the dark... You used mobile BP, and the printed a paper one was left at the main podium counter, making them think you were not in the boarding area nor on board so they offloaded you from the system without double checking on board nor checking the gate reader REC lists... I see many agents in CLE do this and it definitely leads to a lot of Reservation troubles down the road...
But hey that's my guess...
-Cle-