I'm fairly new to muzzleloading, but I think the following are some habits I think are key to avoiding mistakes:
1. Scribe one or more witness marks on your ramrod (may need two marks if you shoot a small volume of faster powder with a light, short bullet, and other times a large volume of slower powder with a long, heavy bullet--but know which mark is for which load).
2. Never load from the box of slugs/bottle of powder. Weigh or dip ALL of your charges ahead of time and put them in speed loaders or plastic vials. After each shot, lay out ONLY the components necessary for the last shot, and in order left to right. When you're ready to load, move through them systematically, so that you don't get a bullet down the barrel ahead of the powder, etc. When you are done loading, and after you have checked your witness mark, check to make sure that there is only ONE empty powder vial on the table. After the shot, put up the empty vial and only then lay out the components for the next shot.
3. Make a habit of never taking your hand off of the ramrod while it is in the barrel and of withdrawing it from the barrel SECOND that the bullet is seated.
4. Keep a T-handle or some other large attachment on the outer end of your range rod to make it more noticeable if left in the barrel.
5. Make a habit of every time, when you first sit down in front of that gun after loading between shots, glancing at the bench to see your range rod and ONE empty powder vial before you lean in and click off the safety.