Marcus Rashford won the spot-kick in the first half at Old Trafford, but the England Under-21 international appeared to go to ground without making contact with Fabianski.
And the Poland international was absolutely incensed, as his manager related after the game.
“He was furious. He was furious," Clement told reporters in the post-match press conference.
"He said: ‘I’ve gone down to get my hands on the ball, and I can see that now I can’t get it so I’ve come away from it and [Rashford has] gone down before the contact.’"
Rooney's penalty came just before half time, giving the hosts a boost after losing Luke Shaw to injury earlier in the half.
However, Jose Mourinho's men could not hold on for maximum points as Sigurdsson struck with just over 10 minutes left on the clock, dealing a blow to the Red Devils' top-four hopes.