Danger Mouse created very unique and original art with his mash-up of Jay-Z's black album with The Beatle's White Album. The bits from the Beatles album were mostly micro-sampled, and not the very recognizable 16-bar phrases like the one in question here.
The entire song "Do It" is built around the first 16 bars of Tempest's Acid Jazzed Evening. A full 16 bars is sampled note for note, including the unmistakeable C-64 arpegios, typical of "oldskool" chip music. The original music appears in the song, the arpegios panned left, and the original melody, note-for-note, panned to the right. The vocal melody is a variation of the original melody.
This is a case where Timbaland took the first 16 bars of a jazzy, obscure chip song, and developed a pop song around them. I actually like what he did with it, but he didn't give credit where credit is clearly due. Danger Mouse didn't try to hide the fact that he used samples from Beatle's songs. He clearly didn't try to hide the Jay-Z vocals, either. The title of the album refers to both. There is a clear difference.
Had Timbaland given credit to the composer, this controversy would not exist.