The 51-year-old felt that there was a handball in the lead-up to Arouna Kone's opening goal, scored a minute before half-time, while he also contested the subsequent dismissal of Pavel Pogrebnyak in the 65th minute.
Kone's opener was followed by another from the Ivorian two minutes later and Maynor Figueroa's goal just after the break wrapped up the points for the away side, before Pogrebnyak exacerbated an already dismal afternoon for Reading by earning a red card courtesy of an ill-fated lunge on Figueroa.
With Wigan leapfrogging the hosts, forcing the Royals into 19th place, McDermott admitted it was a bad day and that their opposition were the better side, though he remained keen to point out the referee's contribution to their loss.
"There was a handball, an absolute nailed-on handball, then their guy headed it in [for the first goal]. The second goal was a poor one from our point of view," he told reporters.
"They got the third, then Pavel got sent off so obviously it was a bad day. With Pavel's sending off, the referee feels it was a poor tackle, that's his decision. Having said that, we have had a bad day, we cannot say that Wigan were not the better side.
"He's made a choice, he thinks it was a dangerous tackle, Pavel's just dangled a leg there and caught him. The referee thinks it was a red card, that it was a dangerous tackle. I know Pavel Pogrebnyak, he is not a dangerous player whatsoever."
Roberto Martinez, meanwhile, was unsurprisingly happy with his team's contribution to the contest and was particularly effusive in his praise of the Latics' defence.
"Delighted is the best word to describe it, we knew how hard it was going to be with the recent results Reading had, and we never underestimated how difficult a task it was going to be," he told reporters.
"I'm so pleased to keep a clean sheet today. To keep out Reading with no shots on target was an incredible effort from all the players, and showed how well they were drilled and focused in their defensive job."