Daniel Bryan suffered a legitimate injury during his match with Randy Orton Monday night on Raw, according to the Wrestling Observer, which is why the match was stopped.
The report notes that Bryan was supposed to win the match over Orton, which would have continued the story of Bryan building a resume of big victories. (Earlier in the night, Bryan floated the idea of eventually challenging for the WWE Title in a scripted promo.)
WWE handled the change of plans by saying Bryan suffered a stinger to his neck/shoulder, which was a legitimate injury. To cover for Bryan not winning the match, WWE followed through on a "wrestler health" story that authority figure Triple H stopped the match out of concern for Bryan's apparent injury. This led to a spontaneous blow-up between Bryan and Hunter to keep Bryan strong as a babyface because he's fought through numerous injuries in his career.
The injury situation appeared to begin Sunday night in Chicago. At the Payback PPV, Bryan sold a shoulder injury off-camera following his Tag Title match loss. According to our correspondent, Kevin, Bryan left the ring favoring his right shoulder accompanied by a referee. He was the only wrestler to exit behind the sound booth and not through the Gorilla position.