The second-leg finished 1-1, allowing Barca to progress to the final 3-1 on aggregate.
But the game could have proved more difficult if a Gonzalo Higuain strike early in the second half had not been controversially ruled out.
"When we scored the first goal it would have been totally different and we feel so many bad decisions have been made against us and we are not happy about that," Xabi said.
"We think we did a good job but decisions went against us, we really feel that way."
The former Liverpool midfielder claimed that Higuain's disallowed goal would have altered the nature of the tie in Madrid's favour as the game was still deadlocked at 0-0 at the time.
"It would have changed everything, our position would have been much stronger and after that it was much more difficult," he said.