Using fill command to empty a small area (using minecraft:air) is typically successful, but certain items get dropped as an item instead of being replaced.

I have done several tests, affected items include:
Ladders, detector rails, activatior rails, powered rails, repeaters, and comparators.
Results seemed inconsistent at first, with said blocks being properly replaced sometimes. I was able to reproduce the effect though.

These items when placed on the bottom of the fill area would be properly removed, but if the were on a level surface 2 blocks up, they were not removed properly. See screenshots.