Rashford went down under a challenge from Swansea goalkeeper Lukasz Fabianski just before half-time.
Wayne Rooney scored the spot-kick to give United the lead, but Gylfi Sigurdsson equalised with a free-kick.
"You want players to be honest and give their best and play hard, but not to do those kind of things," said Clement.
"Having seen it again, the player deceives the referee. It's clear.
"It's not even falling into the challenge. The fall is before the tackle so the referee was deceived."
Clement believes his team are playing with "a lot of confidence" after coming through a spell of six matches without a win to take four points from their past two games.
He felt Swansea had opportunities to win at Old Trafford, particularly a late chance that fell to Fernando Llorente.
"I've spoken to the players and told them how tremendously proud I am of them," he said.
"It's hard enough conceding a goal at that point of the game because it changes the whole complexion, and the fact the penalty was unjustly awarded as well showed that we've got character.
"We had to dig in, we had to defend.
"But it was a fantastic moment of quality from Gylfi, and after that another wonderful chance for Llorente from another set-play, so we're happy with the way we performed."
Swansea host Everton in their next match, then travel to relegated Sunderland, before hosting West Brom on the final day of the season.
"We've come off a rough spell where we didn't play well, particularly against Watford and West Ham," said Clement.
"We have turned the corner now and we're playing better."
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