Was playing today and clearing the plague from the Shallows and for some reason the meter still says there are some enemies remaining, when there are no more to be found. I searched everywhere! Even in the dark area beneath the Shallows.
The bar is not a gauge of remaining enemies, but simply your reduction of the plague and progress toward spawning the Pestilence creature/boss.
You can revisit the area later after enemies respawn, your progress will stay the same.
Shallows have a secret area, catacombs, with even more enemies. You can access it either from the sewer entrance slightly ahead and to the left(you can see the light from the entrance in the top right corner of the image), where this image was taken, or from the dropdoor in the brocken tower where the save point is.
You will need a light source as it is dark in there. Sometimes the boss will also spawn in that area.
His posts specifically says he checked there;
Yes, that worked. Still I was surprised to see only 2-3 enemies in the dark catacomb area. Usually there are more, even when the Pestilence hasn’t taken over the Shallows.
Yes, the catacombs is what I meant by the dark area. So, I’ve already been there. Thanks for responding though.
Hmm, didn’t read till the end, my bad.
Yea, I have had something similar happen to me a couple of times; including the shallows. So I just moved on to another area and looped back later.
The higher the plague intensity, the less progress kills give too. So in small areas like shallows it can happen even if it’s not bugged.
Right now I was playing In Black Trench, not been here since just started the game today.
I spawned at waypoint killed a few enemies to get to fire to raise the plague area to the max. Then killed a few enemies that were still in range of me.
But now the bar is 70% and been walking around the level for 10min none of the other mobs are spawning. I cleared the trench with plague a bunch of times, so i know where they should be spawning, but there is nothing, entire level is empty, and yes the level showed unexplored on the entire map when i entered.
Restarting the game does not make the enemies spawn.
Will now leave the area and go back in few hours, to see if they will respawn…
Please if this happen again we need a clip or a screenshot that shows you have explored everything 
Silas
ok, when i went back 2,5hr later all mobs were there again.
When I was walking around the first time I was wondering if all the monsters fell thru the floor or something 
I know that sometimes happens to a single monster on my screen.
But besides the few monster in beginning of the level, the entire level was empty besides all the ore/trees/chests loot
Is there any way to send a save of a game? This must be difficult since the game will fow/respawn everything based on time.
Perhaps a report bug option ingame that sends the heap dump/world game state might be helpful for devs.
I’m a developer
Great to know you are a developer!
Usually if this bug happens all enemies will despawn. You might have found a variation of that problem.
You are also correct that the Realm state is a snapshot, and will be overwritten at some point. To save and share the moment soemthing important has happened, you should close your game and copy the Datastore with your player-prev.log and player.log.
As someone who is not a developer, or has an IT background that is all the info I have on that subject
So I suggest you do that next time you experience this again!
You can just add to this topic again. Thanks for your diligence DexteR!
Silas