Actually, I almost never find this. I do have this problem constantly with Guitar Hero though. 
 
I haven't played the Hendrix stuff, but I suspect that Hendrix's loose playing technique might not translate in a logical way to a rigid button interface, so the people charting have to find some approximation.  I can think of a few examples of things that both RB and GH struggle with: 
 

• Bending strings: RB usually charts this as a single note for you to use the whammy bar with. GH charts the various notes hit as separate even though the original guitarist wouldn't be moving their fingers that way. Neither is ideal/intuitive.
• Sliding chords up and down the neck: RB did better with this starting in RB2 - they'll make you slide your fingers in a certain shape up the plastic guitar neck. GH will make you hit all the notes in between awkwardly.

^^^ Pretty much everything this guy said.

I think it was GH3 where they charted slides as HO/POs from orange to green (or vice versa), but RB didn't start doing that until RB2 came out.  That was a welcome change. 
 
One guitar charting that always bothered me is the beginning of My Iron Lung by Radiohead.  There's a clear HO/PO in the song, but it's charted as separate strums.  I understand that was a limitation of the RB1 engine, but it's still annoying.  (@0:07):