Enemies get auto-added, and can be manually added again.
There was a rework of the enemies system, so that instead of having to manually pick and choose your enemies (which you can do), if you have empty slots for enemies, ninjas that kill you will fill up your enemies slots so you can enact retribution on them later.
Simplified fight approach deployed
New fight approach deployed, try it out on the fight page.
You can now cycle through new enemies with the arrows and attack directly off of the fight page (instead of making multiple clicks) . Go "back to the fight" and it will queue up the next living enemy for you.