The Potters skipper was involved in an angry exchange with Red Devils striker Robin van Persie as the two sides headed down the tunnel.
The verbal sparring continued behind the scenes, forcing referee Lee Mason to take action.
He entered the Stoke dressing room at the interval and cautioned Shawcross for the part he played in the incident - with the centre-half appearing to have grabbed Van Persie around the neck at the end of the first half.
Hughes, who saw his side succumb to a dramatic 3-2 defeat, admits he was left baffled by the decision - with the Welshman unaware of yellow cards having ever been dished out during the break before.
He said in the Daily Star: "Ryan was booked in the dressing room.
"The referee made a point of knocking on the door and booking him. I've no idea why.
"He pushed him (Van Persie), I think, but I've no idea because I didn't see the incident.
"But he wanted to book Ryan. I've never known anyone get booked in the dressing room before."