The 21-year-old, who made his senior international debut in the 1-0 defeat to Costa Rica on Friday, has left Alex McLeish's squad along with Newcastle United's Matt Ritchie and Norwich City's Grant Hanley.
United tweeted to confirm the player has suffered an injury but they did not specify the extent of the problem.
McTominay is expected to be assessed when he returns to Manchester, ahead of United's Premier League clash with Swansea City on Saturday.
The midfielder has emerged as a key part of Jose Mourinho's first team in the 2017-18 campaign having his made his debut for the club against Arsenal the season before.
Despite being born in England, McTominay opted to play for Scotland at international level, with Craig Brown having suggested that Mourinho may have attempted to dissuade the midfielder from representing the Three Lions.
United are back in action against Swansea City in the Premier League on Saturday although it remains to be seen if McTominay will be available for selection.