You have taken the time to plan the rehearsal, now you need to stick to that plan.
If you are planning on working on tune transitions, don't play the whole lead in song, and the whole next song, pick a point toward the end of the first song and finish as soon as you know the transition was made correctly and you are solidly in the next tune. With that said, work it. If there is something you here related to the transition that isn't right, can be made better -- stop and work it. Do not stop for general clams, or things that aren't related to the transition. If someone doesn't know their part, let them know after the rehearsal that they really need to work on it, but don't stop the rehearsal to let them learn it.
If you are doing a run through, let the small clams go - but do stop for the train wrecks. Keep notes of the clams so you can figure out what needs to be worked on at the next rehearsal, and so everyone knows what they need to practice outside the rehearsal.
As an expansion of what I said in an earlier post, it is important for the designated rehearsal leader to force everyone (including themselves) to stick to the rules of the rehearsal. There may be one player who really wants to go back and work on X, but unless X falls in the framework of the rehearsal, then the answer has to be "NO, but you know what you need to work on at home", or "NO, but we can put that down to work on the next time"