Chelsea lies third on the Premier League standing, two points behind leaders Arsenal and have played United twice this season.
Arsenal still has a game against United, so also second-placed Manchester City.
“Maybe the rules should be adapted for more fairness,” said Wenger.
“It opens up questions about the dates of this transfer window.”
Mata’s proposed £37m move to Old Trafford could be sealed on Friday with the player set for medical at the club training facilities.
United are 14 points behind Arsenal but could still impact on the title race pendulum.
They travel to the Emirate Stadium on 12 February and are yet to welcome City at Old Trafford.
“If you want to respect the fairness for everybody, that should not happen,” added Wenger.
Chelsea agreed to sell the player to the reigning champions, just days after beating the latter 3-1 at Stamford Bridge, their second meeting in the ongoing campaign.
“Some team’s have already played twice against one opponent and some others not.
“I can understand completely what Chelsea are doing. They could have sold last week,” Wenger continued.
The Gunners are currently linked with Schalke’s Germany midfielder Julian Drazler, but Wenger feels the club’s chances of adding to the squad largely depends on finding the right option.
He added: If something exceptional turns up we will do it, but not everyone will strengthen- they buy, but that does not always mean strengthen.”
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