Still happening in 1.6.1 Windows 10 and Xbox editions for sure.
Can confirm seeing the same behavior, appears to happen when there is a lot of ex at the same time. Can reproduce via a mob spawner farm. Kill a number of the mobs then watch as the tool appears to freak out. I am on a realm.
I am seeing the same thing with villager disappearing from my Iron farm. Realms, playing on Windows 10 1.2.8 version.
I have two pods and it appears only one of the pods has villagers disappearing and it appears that the pod is on a chunk border with the line bisecting the villager pod (Pod is 3x2) and the border runs through the middle of the pod on the long side.
I check on the pod every couple of days and it is random as to how many villager s disappear. The Pod on the other side of the farm does not appear to have anyone disappear but that pod is in the middle of a chunk.
Impacts 1.16.2.0 release also parity item with Java. It is not a huge problem but wanted to update the status.