When several entities have several commands constantly running on each (even in ways that barely cause lag) when the entities are in unloaded chunks, then teleporting away from the chunks and returning, can cause the entities to become nonexistant although they physically are still visible. Killing them will return the error "That entity cannot be found" when the entities are clearly visible. Upon teleporting away to unload the chunks again and returning, or exiting and rejoining world, the entities will have finally gone away from being killed.

To reproduce using the world attached:
(Also see attached video)

1. Teleport out into unloaded chunks:

/tp ~1000 ~ ~

2. Summon armor stand that is being affected by commands running in spawn chunks:

/summon ArmorStand ~ ~ ~ {CustomName:CraftingMachineTemp}

You will see several other armor stands being spawned.
3. Teleport further out to unload those chunks (try to do this very quickly after spawning armor stand):

/tp ~1000 ~ ~ 

4. Teleport back:

/tp ~-1000 ~ ~

5. Notice the armor stands can be visually seen. Type

/kill @e[type=ArmorStand]

6a. Armor Stands may actually exist and be killed. In this case, return to spawn and retry from step 1.
6b. Error is returned: "That entity cannot be found" Go to step 7
7. Teleport out to unloaded chunks:

/tp ~1000 ~ ~

, alternatively exit and rejoin world.
8. Return to chunks and kill armor stands again to find that now they do exist again.

--steps can also be found in world file

Notes: removing the majority of the other armor stand spawns, even though few of them have commands running constantly on them, appears to lessen the chances of the glitch.

Lowering the amount of commands running also seems to lessen the glitch chance. Current amount is as low as I was able to go on my computer before the glitch would occur less frequently.

Effect of this bug may or may not be related to the computer as even though there was very minimal lag, it still caused this bug.