This "rumor" is actually fact. The problem is that people, for whatever reason, can't discern the differences in someone's writing being used/credited on an album and someone helping/submitting input for an album.
Big Sean was most definitely there in the studio with Kanye during the production of Graduation. There's a video floating around somewhere that shows behind the scenes clips of the Graduation era, like when Ye played Big Brother for Jay-Z a while back. One of the clips shown is of a Black woman (can't remember the singer's name) and Big Sean next to her sitting on a chair and they are trying to write the bridge and background vocals for "Champion."
The girl then starts singing her idea out loud to see if the others approve, going "this is the story of a champion... Stand up stand up, here he comes..." The way Kanye and many other artists work with teams is that 4 or 5 writers will be assigned the task of making a certain part of a song. Then either each writer submits their ideas over and over again until one gets approved, or all the writers form a consensus on one idea an submit it to the main artist or executive producer.
It's pretty safe to conclude that Big Sean did in fact work on Graduation but none of his ideas were implemented, therefore he has no credits on the album.
And this isn't ghostwriting either. It kind f is but it's much more subtle and has very minor effect on the final product. Kanye has never used a ghostwriter in the more commonly referred to sense where one or two people other than the main artist writes an entire verse or song.