The Aquilotti suffered a 2-0 loss at San Siro with Lautaro who got his name on the scoresheet converting a penalty kick in the second half.
However, Motta believes the Argentinean striker should have seen red before the break.
The striker reacted after a contact with Martin Erlic, hitting the Spezia defender’s chest with his shoulder.
“I usually don’t talk about referees. I don’t want excuses,” the former midfielder said.
“However, I don’t understand how the referee managed the contact between Lautaro and Erlic. He hit him on purpose. To me, he deserved a red card. These incidents can change a game.
“I don’t understand what happened there, even with VAR. Lautaro then converted the penalty kick. I am more surprised than angry.”
However, the former Italy midfielder is satisfied with his lads’ performance in Milan.
“It was a good performance against a great team, maybe the best one in Serie A. We did what we had prepared, we tried to remain compact and we stayed in the game.
“I think Inter fans for their warm welcome. I was focused on the game, but I will never forget what we achieved here together.”
Thiago Motta spent two years and a half at Inter, scoring 12 goals in 83 matches. He was part of the team that won the treble under José Mourinho in 2009-10.