Hill sent off Reading defender Alex Pearce in the ninth minute for fouling Benik Afobe and conceding a penalty, which Wednesday's Chris Maguire converted.
"There's only one talking point in the game," Adkins said. "The referee, wrongly in my opinion, sent off our centre-half.
"Having looked at the video footage, I'm not sure it's even a penalty. Alex said he didn't touch him. Okay, the referee gives a penalty, but there's no way it should have been a red card.
"That totally changed the complexion and outcome of the game. It was a ridiculous decision and that was a major factor in us not winning the game today.
"I've got a group of players who have put in another hard shift and it's a shame for them because we have had good momentum lately."
Reading had won four of their five previous matches, scoring 16 goals, and could have gone ahead early on in the Sky Bet Championship fixture.
Adam Le Fondre, who had claimed hat-tricks in the previous 7-1 and 5-1 home wins over Bolton and Blackpool respectively, scuttled through and tried to bypass goalkeeper Chris Kirkland but was denied when the Wednesday captain dived at his feet.
Pavel Pogrebnyak should also have done better when managing only the merest of touches to divert the ball past Kirkland. As it trickled towards the goalline, Wednesday centre-back Miguel Llera was able to get back to clear it to safety.
Reading soon paid for those two misses when Pearce appeared to bring down Afobe.
Maguire slotted in the spot kick and Wednesday rarely looked back. They dominated the rest of the first half and could have stretched their lead, with Afobe - on loan from Arsenal - striking the top of the crossbar and Maguire forcing a fine save from Reading goalkeeper Alex McCarthy.
It was McCarthy who played a major role in Wednesday's second goal in the 58th minute, when he fumbled a tame effort from Maguire. Afobe followed up to bundle in his first goal for the club and help stretch Wednesday's unbeaten run to 11 matches in all competitions.
Stuart Gray, the Wednesday manager, disagreed with Adkins' verdict on the red card.
"I thought it was the correct decision," Gray said. "Perhaps we had a bit of luck in the first five minutes, when they missed their two chances, but I thought we dominated after that.
"I'm grateful to Arsenal for letting us have Afobe. He's got real talent and caused Reading a lot of problems with his pace and power.
"But it's not really fair to pick out individuals. It was a collective team performance. With a bit better finishing, we could have finished them off earlier."