clone, fill, setblock leaving behind ghost entities

I have attached a copy of an unreleased map to help with replicating the bug in confidence. It has detailed instructions how to reproduce the bug within the map. Please do not share it.

Tile entities such and chests and signs sometimes remain after a fill or clone command is performed that should be overwriting them.
I've noticed it happens a lot more after teleporting in and out of the area, also if there are either a lot of entities or if you're doing multiple fills/clones on the same area.