Relates to/Duplicates:
MC-44904

Found the reason:
Summon multiple mobs with the same UUID

/summon Pig ~ ~ ~ {UUID:1-1-1-1-1}

When using:

/kill @e[type=!Player]

the game thinks it killed all mobs (even the ones with same UUID) and you get also the same count of reports like there are mobs

Killed Pig
Killed Pig
...

When you hover them they have both the same UUID

BUT actually only one of them was killed.

So you get the error message: "That entity cannot be found"