The Spurs are definitely under-sized and that does lead to problems especially in offensive rebounding by the opposing team.
Most notably:
1) Remember in the Playoffs last year, Diaw was crushing Finley and Udoka? Same problem this year with a Shaq, Amare, Diaw, Bell & Nash/Barbosa lineup.
2) Against the Lakers, Bowen covers Kobe so that leaves 6'5 Ime, Manu, Finley, etc on 6'10 Odom. Duncan on 7' Pau and Oberto on 7'1 Bynum
3) Against the Blazers, Bowen will cover Roy, so that leaves Travis Outlaw at 6'9" and very athletic covered by a little one
4) Against the Hornets, only CP3 is small, Posey, Peja, West and Chandler are all 6'8 plus
5) Rockets are huge as well Yao, Scola, Artest, TMac...only Alston is small
With the lack of size on the Spurs, the only counter to the size would be to play small ball.