The Hammers boss was left wondering why his team were not awarded a penalty when the ball appeared to strike Arsenal defender Gabriel Magalhaes on the arm inside the box.
The incident was quickly checked by VAR but play continued without punishment, despite a similar decision resulting in a penalty being awarded against Manchester United defender Victor Lindelof just hours before at Old Trafford.
The incident, which occurred while the scores were level at 1-1, proved crucial as Eddie Nketiah struck a late winner to condemn West Ham to defeat - a result Moyes said his side "didn't deserve".
But the 57-year-old feels the rules must be clarified on handball after changes from the International Football Association Board (IFAB) for the 2020/21 season.
"I think it was a penalty," he told BBC Sport. "If it wasn't they need to explain the rules to us again. We’re all unsure.
"You don’t know either [he said to the interviewer]. He should have headed it, because he missed it, it hit his arm. He should have been punished for that."
Moyes added: "I think the goals could have been chalked off for offside."
Moyes was, however, happier to see an improved display from his side after watching his side outplay Mikel Arteta's men at the Emirates Stadium.
"We asked for a better performance and we got it," he added.
"Everyone who watched that would ask how West Ham didn't get the three points. The answer is we turned off and we missed a few chances. We don’t deserve to lose this."