Users of the software had a free copy of the new album automatically downloaded to their accounts as part of a marketing stunt in September that tied in with the release of Apple's new iPhone.
U2's latest album Songs of Innocence was given away free but the marketing stunt backfired, reported Contactmusic.
The apology was prompted by a criticism from a Facebook user during a question and answer session. "Oops, I am sorry about that," said Bono.
"I had this beautiful idea and we kind of got carried away with ourselves. Artists are prone to that kind of thing. Drop of megalomania, touch of generosity, dash of self-promotion and deep fear that these songs that we poured our life into over the last few years mightn't be heard.