Mistake 1: Since the party was epic level, the idea was that they'd eventually figure everything out, maybe going a little mad in the process, and kill Cthulhu.
Mistake 2: This is the Forgotten Realms. Why haven't all the other epic NPCs done something about this?
Mistake 3: Letting them do interesting subplots when they were supposed to be on a deadline when the big C was supposed to wake up. Then losing track of the time.
As someone who's run a FR/CoC crossover (albeit not at epic levels), here's my notes:
On Mistake 1: Not a bad plan, but I tend to like the feeling that they can't do jack a bit better...Cthulhu is gonna come get ya...all you can do is hope that not EVERYONE goes mad...you have to pass under his notice, not up in his face (especially tough for people used to bashing evil about the face a bit...this ain't no FR organization that exists mostly to get it's butts kicked, heh.). It works especially well for epic levels -- they have to use their powers just to ensure that the local farmhands don't get lost within their own pscyhes, nevermind beating Cthulhu...where's the fun in winning if the world is ash behind you?
On Mistake 2: My answer was that they're all somewhat magical/blessed by the Gods. When the Gods are all killed right in front of the believers and magic starts driving you insane whenever you use it, well, Elminster can't walk around his house without becoming a gibbering ball of goop....
On Mistake 3: What, time's supposed to make sense to them? Hehehe, these are Elder Gods, they're supposed to be unpredictable. You expected the Convergance to happen Sunday? TOO BAD, it happens Saturday while you're on the can!
Needless to say, I really really enjoyed making the Realms gibber with madness, and the PC's took great joy in seeing a beloved campaign world torn asunder by another. They're thinking of returning, sooner or later....won't that be fun?! We're thinking of using d20 Modern rules for extra deadliness and no magic, but a bit more archetypal than 'investigators.' Then it's just a matter of seeing how long Cthulhu lies dreaming...(mwahahaha!)