So I’ve run into an issue recently where I can’t seem to get my stations to automatically upgrade their weapons. I learned that one issue is that if you have a net loss on the exotic/unique resource required for the upgrades, it simply won’t upgrade. I fixed this immediately and have kept an eye on it since a recently failed run. (Relatively new to the game and completely new to the subreddit so sorry for any ignorance) Even though I have a +5 to +10 for some of my resources they still don’t upgrade. Someone suggested that demolishing modules on the stations and rebuilding those modules would update the weapons and shields/armour. This only partially worked and maybe even backfired, and now I have a citadel with the following:

Tier V, IV, and III armour and shields. Tier V, and III missiles Tier III torpedoes (Weren’t at all present before) The Tier V gauss cannons downgraded to tier IV

This all occurred when I demolished a missile module and rebuilt it. I have the best reactor available to me through the usual tech tree (I think it’s the zero point reactor) Which was another suggested source of the issue, that the station couldn’t power it all.

Now I must admit I got what I would like to think a lucky start because I found almost all the unique resources except for two early on and I am harvesting all the ones I can. I have a massive stockpile of exotic gases, motes, crystals, and even some living metal/dark matter. I even have Zro in my empire’s influence but I cant harvest that.
This is the vanilla game as I haven’t purchased any DLC or mods for Stellaris.

I must also mention others have experienced this but the very short search I did came up with short conversations that are close to a year old. So my knowledge on the matter maybe outdated.

Any information is helpful, including those who may be suffering from the same issue.