Manchester Evening News reports that the English full-back was not with the squad before kick-off.
The former Crystal Palace defender was instead seen in the director's box.
This is despite the defender having been named among the 12 substitutes for the clash with Sociedad.
Wan-Bissaka had missed the Red Devils' 2-1 win over Arsenal and the prior 1-0 victory over Leicester City through a "small complaint".
There have been question marks over the future of the right-back, with Diogo Dalot having displaced him in the United XI.
He arrived at Old Trafford from Palace back in 2019 for £50 million but has found game time hard to come by in recent times.
Wan-Bissaka made 26 appearances last season and has made just one appearance so far this campaign, a four-minute outing.
Reports claim that United boss Erik ten Hag was willing to part ways with the right-back but the club's football director John Murtough blocked the potential departure.
West Ham United and Crystal Palace were interested in Wan-Bissaka but he has stayed put at Old Trafford.
He has two years left on his current deal with Manchester United but speculation is growing over his future.
Dalot enjoying competition from Wan-Bissaka at Manchester United
Dalot feels that the competition being posed by Wan-Bissaka is helping him improve.
He was asked for his thoughts on Wan-Bissaka rivaling him for a starting berth under Ten Hag before Manchester United's disappointing defeat to Sociedad.
He said (via SportBible):
"When you have good competition, I like to call it health competition. You can see this season we have very good players in each position, which makes us better as a team. We have a lot to learn together, we have a good squad."
It remains to be seen if Wan-Bissaka will be afforded more game time this season given he has missed action through injury.
However, the fact that Ten Hag was open to offloading the player this summer speaks volumes of how he views the Englishman.
Wan-Bissaka was a regular under former manager Ole Gunnar Solskjaer, with the Norweigan having signed him in 2019.
It was under former interim coach Ralf Rangnick where the problems began for the English defender.