the only other ones i can think of are the anti-module ships and colonizer ships. Those, plus what stormsong listed are not supposed to auto-join. if you really want them to, i think you might be able to turn it on for that ship, but to do what you want you'd have to turn it on after its built but before it arrives in the same well as the fleet.

The more annoying problem is ships auto-joining the wrong fleets. as soon as they enter a well where there is a fleet, they auto-join. even if the rally point is set to a ship and that ship is part of a fleet.

if they are built in the same gravity well, that might be the issue. Anyhow, there are a lot of issues with fleet joining that are frustrating and most of us dont use fleets. I really insisted on using fleets for a long time, but then I realized how much time I was wasting just trying to maintain it.

Yarlen:  See the same save file I just sent for your request on forum: https://forums.sinsofasolarempire.com/405965.  That issue has also occured in that file.  Now that I know you are looking for save files like this, I will start to save a version of the game each time a new issue arises and not save over it from that point forward.  I assume that will help in tracking down the issue.