I’ve never played Phoenix Point with mods. In fact, I didn’t even know it had mods.
The bug with the artifacts alerts on the geoscape is a bug that Snapshot shipped with their DLC. It started after I saved the game with an alert on the screen. When I loaded back in from the save, I received the shown broken alerts for every single ancient site that I owned.
I didn’t report it because I just couldn’t bring myself to care with all the other bugs I was encountering. That being said, while anything is possible, I strong suspect that those broken alerts are not a symptom of the same bug that causes my players to load into a Citadel mission injured. I played a Citadel mission way before the bug with the weird times and also had some fully-healed soldiers load in with small amounts of HP missing. I assumed at the time that I didn’t fully heal them before heading out, and didn’t think much about it
I think the bug is more likely related to the overhaul and changes that were made recently to the Citadel missions. There used to be a completely different map that all Citadel missions used. The map was changed, and it stands to reason that other changes were made too. Every single mission I have played this playthrough in a Citadel has had this problem, but the amount of lost HP was less, and no body parts spawned knocked out.
It looks like a bug is capping the HP on this map at 200, because all soldiers with over 200 hp are reduced to 200. I can load the save right before I start the mission, and head to a nearby Lair, and no one loads in injured, so this is definitely Citadel-related.