Forlan had already represented Atletico Madrid in the qualifying rounds of the Europa League meaning he won't be available for Inter until the New Year at the earliest.
But Inter failed to realise this, listing him in their 25-man squad submitted to UEFA.
That meant there was no space for teenage forward Luc Castaignos on the list and now Inter cannot field either player.
"I'm sorry mostly for Castaignos because otherwise he could have played," said Moratti.
Inter bought Forlan as a replacement for Russia-bound Samuel Eto'o, presuming he would be available in the Champions League.
Now, not only does their forward line look weaker without the Cameroon flyer but they will have limited attacking options in the Champions League group stages.
Moratti says he understands fan frustrations but claims Eto'o's sale was necessary.
"The fans are very sensitive to big problems and the difficult moments the club finds itself in, and of course sometimes they can't help but show their dissent," he said.
"I understand that, it's human. The financial fairplay forces painful decisions to be made to come back within the parameters.
"But I'm convinced we'll still be very strong. There could still be some doubts about the new system but I think it's the right way for the team to evolve."
Moratti was referring to new coach Gian Piero Gasperini's preference for a three-man defence.
That has caused some consternation amongst fans but Moratti believes Gasperini deserves time to make it work.
"He will be successful with the tactical evolution he's implementing and if it should happen that it's not successful, our coach is intelligent, if he thinks it's necessary, he'll change it.
"I'm very confident about the league while we will tackle the Champions League game by game given our difficulties there.
"The important thing is to never go onto the pitch thinking you're world champions, in football it's vital to be humble and have the desire to start over, even after great victories."