Atletico and Arsenal played out a 1-1 draw in the first-leg of their Champions League semifinal, with the visitors' complaints centred on Ebere Eze's late penalty claim being overturned by VAR.
Arteta said afterwards: "Speaking to the boys and understanding the penalty incident for the second goal getting overturned. It was against the rules and I don't understand it. Very upset. There is clear contact; he makes the decision and you can't overturn it when you have to watch it 13 times.
Asked if the referee was influenced by the actions of Atletico coach Diego Simeone, he continued: "I don't know. That's an answer for him. It's the wrong decisions and it changes the course of the tie."
On Atletico's penalty, Arteta said: "It is a rule and they have been quite consistent with that. I have nothing to say on that. The one I have to say is the penalty.
"There are a lot of positives. A lot of very good things that we did. We knew we would have tough moments. Their home record is once again.
"We are in an incredible position. We have to play in front of our people. It is in our hands."