It looks like you have identified an area to work on, short bowling. You have 2 options
Practice
It is very hard to practice against as in the nets most bowlers pitch it up and bowling machines are usually set so you can simply drive the ball.
If you can get someone to bowl short, do some throw downs or get in a bowling machine you can work on your technique ... Keeping the ball down
Decision making
You can chose to decide that early on you or prone to getting out to short bowling so try not to hit it too hard, place it for a 1 or 2 or just leave it.
I get the feeling these short balls are hop/chest high and not flying towards your throat at pace so you are seeing them as a free hit and just going at it very hard??
At club level bad balls often get wickets as batsmen get a little excited and really try to smash it