Did we ever find out why we can't trust the captain and who left the note? I assume it was Michael, but I still don't understand why the captain couldn't be trusted...
I'm still wondering about this as well. It could have been Michael, leading them in the wrong direction. Or it could have been Lapidus, who seems to be questioning everything about the freighter's trip to the Island.
My vote is that Michael left the note as well. Michael had been told by Tom that it was Widmore who planted the fake wreckage; the captain believed it was Ben's doing. Assuming Michael knew the captain held Ben responsible for the wreckage (though I'm not sure how he would know, really), he might have left the note to warn Sayid and Desmond not to believe the captain's story.
It's crazy, but I'm not really convinced this is Widmore's doing just yet. They've told us outright that the freighter's his and they never tell us anything outright. Could Ben have set this all up? His long con? It just seems to easy.