I had a mission that was -not- Gatecrasher resulting in getting a sharpshooter from a rookie promo.

This was after restarting a mission. Do I have to enable it / un tick re tick every load? This pesky sharpshooter keeps appearing ;D. I checked after the promotion was given whether or not it was unticked, and it was. So maybe it just didn't acknowledge it.

Thanks for the report, marshmallow justice. That's really odd that a disabled class would show up in that screen, in particular. When you say you restarted the mission, you mean just loaded an earlier save? I wouldn't think that reloading the game would affect it, but I'll check when I have a minute to make sure. On a different note, do you have any mods that might swap out the 'After Action' screen?

If you have the 'Restart Mission' mod, beware - using it seems to disable all active mods until you next return to the campaign map. Might be that?

(Not the modder's fault either - it's the way the button was made - hardcoded not to check for mods, which is probably why it was only available in the first mission in vanilla!)

The menu seems to be duplicating certain class mods and producing blank classes

I disabled the Ranger class (like any sane person would), yet the game gave me a post-mission Rookie promotion into a Ranger.
It was after the first Council mission I received, which was my third mission overall. (Gatecrasher -> Guerilla Operation -> Rescue a VIP. That third one.)
The Rookie was not one of the initial starting roster, but rather one I received from scanning a thingy on the world map. (Not that I think that this is actually relevant... but hell if I know, so I'm just throwing all the info at you that I can.)

Also, which is noteworthy: I also disabled the custom Necromancer class (for purposes of "I'll only train those manually once I build a Psi Lab - for immersion!"), and it DID skip that one.

Which is to say, it gave me one promotion into each of my enabled classes and then went ahead and gave me more promotions into classes I had already - and while it didn't give me a Necromancer, it did give me a Ranger for some reason.

Thanks for the report. I don't think it should matter where the rookie came from. I'll take another look and see if I can discover how disabled classes are sometimes slipping in there.

I actually think I found the reason.
Pressing certain buttons, like the class buttons and / or the apply button, multiple times in the mod menu seems to be what causes the problem.

I enabled everything, clicked apply, closed the menu...
... and then I went back in, disabled the Ranger and Necromancer with exactly one click each, clicked apply exactly once and then left the menu - and lookie there, that solved the problem.

I won't try to replicate it just in case it's actually something else... I don't wanna mess around with the working state right now.

But you try it - just try and press different buttons and checkboxes on the mod's menu multiple times, and see if that messes things up.
I'm pretty sure that's it.

The disabled class that always pops up for me the Trooper class (from the trooper mod). I only ever get one though. It seems to be at random, I just end up with one trooper in every campaign.

Hi I have not the option for the insane. I have for the soldiers.