Recently I have lost three inner tubes to the same problem, damage round the base of the valve. I'm not sure what is causing it buts its getting really annoying. Using specialized inner tubes, road bike (Specialized allez sport) with mondo tyres.
I've had a couple of suggestions: Tyres not at a high enough pressure Need to talc the inner tubes.
This has been asked recently. It may pay to use better quality tubes, Michelin or Conti, with Presta valves. Check the rim for sharp edges where the valve stem comes through the rim. Check the quality of the rim tape in the same area.
you might want to try removing the little lock screw that locks tightens the valve stem to the rim. Sometimes those will pull a portion of the tube into the valve hole and create a flat.
Pumps that have hoses are much less likely to damage tubes than pumps that attach solidly to the valve stem. It's also better to be as gentle as you can when removing the pump chuck from the valve stem.