A brace from Mauricio Pinilla condemned Inter to their fourth defeat in six league games.
Stramaccioni believes that his side were on the wrong end of a contentious penalty decision after Matias Silvestre was cautioned for a foul on Pinilla early in the second half.
He told Radio Rai: "I still must congratulate my team despite a negative result. What's going on is unbelievable. We had a chance with Tommaso Rocchi, then we picked up yet another injury, this time to Walter Gargano.
"Then they were awarded a penalty, which to us looked dubious, before we lost [Yuto] Nagatomo to injury after only a few minutes. With the score at 1-0 the only way to have more of a presence in the penalty area was to send on our biggest aerial threat, Walter Samuel.
"This season is jinxed, but we were doing well until the penalty. Is our Champions League dream over? Now we have a very important match, we've lost another two players and we'll try to go into the Roma game in the best way possible.
Inter have slipped to seventh in Serie A but must now turn their attention to a Coppa Italia semi-final second leg against Roma in midweek.