The one that comes to mind for me is Growing Up In Public by Lou Reed. Although I have to admit, that album was 10 years old before I ever saw or heard of it (so I can't speak to if it affected anyone at the time it was new).
The Beach Boys were very big in the UK in the late '60s, a lot bigger than in the US. But granted that's a long time ago now.
I know that's been mentioned on a number of "bad album cover" lists, but I can't recall why some folks don't like it. Some of the albums being mentioned in this thread probably received a lot more attention because of the covers than they would have otherwise.
A really good example of this phenomenon is the album "my beauty" by Kevin Rowland on Creation records in 1999. I remember this album tanked and this was put down, at least in part, to Mr Rowland's rather unusual choice of apparel for the cover pic!
How many people were saying, "Man, you know what I can't wait for? A(nother) solo album by the singer from Dexy's Midnight Runners" --Another because he put one other out, 11 years prior, not so long after Dexy's successes, so that more folks might have known who he was, and that one tanked, too.
While it's a nice photo I don't believe Pearl Jam's putting an avocado on the cover got people excited over it (Discogs photo).
How about "From Genesis To Revelation"? According to legend, a lot of record stores put it in the religious section, since there wasn't much info on the cover.
Was that cover the debut of the Beach boys script best known for appearing on the cap that's surgically attached to Mike Love's head?
Paul McCartney (who has always loved Pet Sounds) told Brian Wilson, "You really should take more care with your album covers." Brian must have taken his advice, based on the covers of Smiley Smile, Wild Honey, Friends, Surf's Up, and Holland. Those are marvelous covers. Alas, artistic as they were, they didn't help to sell the albums, as great as they were and are.
Jay Ferguson referred to the cover of Jo Jo Gunne's Jumpin' the Gunne as "the album cover that killed the band."