Lukaku missed the final three games of the Premier League season due to an ankle injury, but returned to the matchday squad at Wembley - albeit only as a substitute.
Mourinho suggested that Lukaku himself had decided that he could not start the game, appearing to question the Belgian's commitment to the club after they fell to a 1-0 defeat at the hands of his former employers.
"When a player tells you he's not ready to play, that he's not ready to start the game, then the question is 'how many minutes do you think you can [play]?'" Mourinho told reporters at his post-match press conference.
"How can I convince a player that is not ready to play?"
Lukaku will be part of Belgium's squad for this summer's World Cup in Russia, where they have been drawn alongside England in the group stages.