You can get injured doing anything. We ve seen players injure hamstrings running to first, son sprained back muscle hitting BP, etc.
make sure son starts out slowly if trying new program. Conditioning does not happen in a wk. no reason for kid to hit for hours. If son is having problem or needs work look for good local hitting coach and work on some things. With 20 kids on a Summer team him getting 2-3 possible innings 1-2 times a week may not be enough.
He's 16, is he wanting to play at next level? If so, will he have opportunities this Summer to be seen by colleges?.