the Faction disease

Im puzzeled by the Affliction disease /that turns normal citizens hostile, with occasionall flesh blobs

Its present in Shing Jea island. But on Canthas mainland the hostile people are no where to be seen (unless you count Amn Fa & Jade guild). Only deformed monstrosities, Shiro switched tactics obviosly
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It would have been much better (and scarier) if peacefull (green) townspeople npcs attacked, rahter than the deformed monstrosities.

Initially playing i envisioned a mission/quest where the purpose was to save as many townpeople as possible... and a cure for their aggressiveness. Oh and killing aggressive citizens also decreases the number (so its best to avoid killing as many as possible) however since the aggresive citizens is a threat to nonafflicted... not killing could also result in failure

After that mission Shiro could adapt and only start using corpses for minions...

Now it just seem the disease went away with no good explaination and Shiro started using corpses instead of living ones.

Yay plotholes!!

There seem to be a good number of plotholes in the campaigns. They can't do anything about them, because they can't make a new mission.

I think it's like this: all afflicted were living people. They just start off looking normal and eventually look like The Afflicted. It's like countless horror movies, where one minute your friend who was bitten by that zombie is fine, next minute he turns into a bloodthirsty drone.

I think the reason why there are normal looking citizens who are afflicted is because the disease has been on the Canthan mainland for a while, but it only has just broken out on SJI.

the above is correct and addressed

There are a few occassions in the mainland inwhich you will find "normal" people mixed in with the afflicted mobs.