The Nerazzurri were on course for victory at the Stadio Olimpico, despite playing with 10 men from the sixth minute on due to a red card for goalkeeper Samir Handanovic.
"The refereeing left us somewhat perplexed," Branca told Sky Sport Italia. "It was a great game and hard-fought, so it deserved a better refereeing performance.
"We can start from the penalty, then a few free kicks given and not given. We are not contesting the spot-kick, but a yellow card would've been enough.
"It's a shame for the players and the coach after a game like that to drop points, especially after an undeserved defeat to Roma."
Inter are fifth after eight games in Serie A.