The Scottish boss was not happy with the Latics' opening goal, but was delighted with his side's second half performance as they rescued a point with a penalty from Leighton Baines
Wigan took the lead in the 10th minute through Ivorian striker Arouna Kone's close range header, but Moyes felt the striker was in an offside position when he met Shaun Maloney's front post cross.
"I think we had a really rough day with the decisions today," he told reporters.
"What we got, we earned ourselves. The first goal [from Kone] was offside, definitely, half a yard offside.
"The linesman is nowhere [near] in line. I've had a look and he's three or four yards behind the ball."
Kone's strike and a Franco Di Santo effort in the 24th minute saw the hosts lead 2-1 at the break, but a half-time dressing down from the Scot inspired the in-form Toffees, and they were rewarded for a good second half performance as Leighton Baines scored from the penalty spot in the closing minutes.
"A thoroughly deserved point," Moyes continued.
"We didn’t do enough [in the first half]. We played really well in the second half, Kevin Mirallas has a great chance and the keeper's made a great save.
"They've done what we asked in the second half which was to make sure we got something from the game in the end."
And Moyes was full of praise for former Wigan man Baines as he calmly stepped up to fire home another late penalty against Roberto Martinez’s side.
"[Baines'] penalty was fantastic," he added. "His performance was up there with as good as anything.
"I'm glad he didn't miss today."
The point maintains Everton's good start to the season, but dropping two points has seen them slup to third place in the table behind Chelsea and Manchester City.