Even if you choose to infer that Trump intended for those two thoughts to be connected (1. instruct AG to appoint special prosecutor, and 2. put Hillary Clinton in jail), Trump would still be overstepping his authority. The President doesn’t get to “instruct” the Attorney General to appoint a special prosecutor.
Here’s an analysis of that hypothetical situation: http://fortune.com/2016/10/10/donald-trump-special-prosecutor-hillary-clinton/
But even inferring that Trump meant Clinton should be in jail only after due process is a bit of a stretch. Many of us watching the debate felt that wasn’t what was communicated. Trump said what he said about jail only because he knew it would score points with his fans. Remember that these are the same people who gleefully chanted “lock her up!” repeatedly at the RNC.