It may have more to do with how he receives the ball, than pitch location. Also, with a low pitch besides being off-balance, it takes a little longer to get the glove beside his right ear and square his shoulder to the target, he may be trying to rush it.
The great thing about the transfer is that it can be practiced almost anywhere, anytime. I see lots of kids waste lots of opportunity to work on their transfer and load mechanics.
Start with playing catch. Every time the ball is caught, there is an opportunity to work on transfer and load. Most kids I see playing catch in practice or pre-game just catch the ball, and lazily load up and throw it back.
Tell you son to use this opportunity to practice the transfer and get the ball into throwing position. THEN he can take his time and throw. Do this EVERY SINLGE TIME. Make it a habit of how he warms up and prepares pre-game.
Second, keep a glove in the TV room. No better time than otherwise wasted TV hours to practice the transfer. No need for a catch - just have the ball in glove and work on the proper transfer and route to throwing position.
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