While most of United's top players were benched or rested entirely for the English League game against third-tier Northampton on Wednesday, Rooney played the full 90 minutes less than three days before a big Premier League match against champion Leicester.
There could be two explanations for this selection: Mourinho either wanted his captain out on the field to lead the team in a potentially tricky away cup tie; or there's a chance Rooney could be left out at the weekend.
"Goals," came the reply from the stern-faced Portuguese coach, both times.
United won 3-1 but Rooney, who started the match as a central striker before dropping deeper in the second half, did not score.
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The Rooney dilemma where to play him, if at all is hanging over Mourinho and won't go away, because it's the most hotly debated issue in English football at present.
Rooney was restored to his favored No 10 position by Mourinho for this season, after finishing last season as a central midfielder for United and England's national team.
Pogba is being played as one of two deep-lying players in central midfield, with Rooney ahead of him, even though the France international is better suited in a three-man midfield that allows him more freedom to attack and not be overly concerned with his defensive responsibilities similar to how he played at Juventus.
It seems strange to spend USD 116 million on a player and not adapt the team to his strengths.
But his tendency to improvise on a whim can also unbalance teams. For example, if Ibrahimovic is dropping deep to get more involved in play then that space is already being occupied by Rooney.
Given the presence of Pogba and Ibrahimovic, a 4-3-3 formation with no authentic No. 10 could be the way forward for United.
Rooney, who has been at United since 2004, has had his moments this season, notably setting up Marcus Rashford for a last-minute winner at Hull and also supplying a brilliant right-wing cross that Ibrahimovic headed home in a victory against Southampton.