On d7, the knight eyes c5, e5 and b6 (sometimes helpful since the Be3 looks at b6), while the c-line is open for the Rc8 and the diagonal a8-h1 is open for the Bb7.
On c6 it's generally just misplaced. There are lines in the Classical where Black plays Nc6-b8-d7...
There is a hybrid najdorf in the line with 6.Bg5 where black plays Nc6. It has become more common in the last decade or so but personaly i dont rate it too high. Anywho, in your game 7...Nc6 certainly seems out of place but i should also point out that your 7.Nf3 (although perfectly playable) is very tame. usually in the line with Be3 the f3 is reserved for the pawn.Maybe your opponent was expecting Nb3 and got confused, or maybe not 
Somebody played the Najdorf line below against against me in a tournament recently. Why is 7...Nc6 so rare? There are only about 10 games in CA's hugebase with this move. I don't know the Najdorf very well, and thought this might shed some light on the ideas behind it.
1.e4 c5 2.Nf3 d6 3.d4 cxd4 4.Nxd4 Nf6 5.Nc3 a6 6.Be3 e5 7.Nf3
Nc6
Any insights would be appreciated.