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Well,  it is unlikely that 3...Nc6 loses by force (hence "punish" is already a slightly inappropriate mind-set) but it is what the old theorists used to call "anti-positional", i.e. it went against the old rule-of-thumb that in d4/d5 openings, neither side should block their c-pawn, since the c-pawn is useful for  both attacking the enemy central space (c2-c4 / c7-c5) or defending your own (c2-c3 / c7-c6). 

The best places to start to get a feel for this are probably the many 1 d4 games annotated in "Logical chess move by move" by Chernev, or maybe the relevant sections in Fine's "Ideas behind the chess openings".

Of course, modern practice has unearthed many playable lines where one side or the other goes against this guidance (Tchigorin Defence, Ragozin System,  Zurich Nimzo, Bogo, Richter-Veresov,  Barry Attack...) but I suggest most strong players must feel  that there is some truth in the old "rule", hence for instance the relative lack of popularity of say the Richter-Veresov compared to the Queen's Gambit.

OK, so how to deal with 1 d4 d5 2 c4 e6 3 Nc3 Nc6? 

Well, you could regard this a  Tchigorin (1 d4 d5 2 c4 Nc6) in which Black has voluntarily blocked in his queen's bishop - hence natural development should allow White to retain an edge. Or it is likely to transpose to a Ragosin - playable but very demanding of Black's skills - just look at Fischer's bad score with it. 

An example of sensible play by White:

Psakhis,L (2535) - Sahovic,D (2425) [D53]
Lvov Lvov (4), 1984
1.d4 d5 2.c4 Nc6 3.Nc3 e6 4.Nf3 Nf6 5.Bg5 Be7 6.e3 0-0 7.Rc1 a6 8.a3 b6 9.cxd5 exd5 10.Bd3 Bb7 11.b4 Nb8 12.Qb3 Nbd7 13.0-0 Rb8 14.Bf4 Bd6 15.Bxd6 cxd6 16.b5 a5 17.Rc2 Re8 18.Rfc1 Nf8 19.Ne1 Ne6 20.Be2 Ng5 21.Nd3 Nge4 22.Nf4 Nxc3 23.Rxc3 g5 24.Nh5 Ne4 25.Rc7 Re7 26.R7c2 Re6 27.Bg4 Re8 28.Qd3 h6 29.h3 Rf8 30.f3 Nf6 31.Qf5 Nxh5 32.Bxh5 Qe7 33.Rc7 Qxe3+ 34.Kh1 Zeit 1-0

Note Black's 11th!

Hope this helps!