https://i.imgur.com/EEweW9T.png

This is cosmetic and doesn't prevent any buildings from being placed in that area.
But it also is visual clutter preventing seeing what else is being built there.

Perhaps a separate Digitizing Tank for fluids would be a better option rather than incorporating it into the chest

Works fine on my end for both deconstruction planner and manual mining, everything is cleaned up.

Are you on the recent version? Are you running other mods that could remove or teleport entities?

Edit: ok, I've found a possible problem with construction bots, 2.4.0 fix should remove all orphaned pipe connections and prevent any new from being left.

The latest update seemed to have resolved it, and any left over pipes have been cleared.

I was using the Decon planner with Editor Extension bots, which work instantly (usually next tick).

Perhaps a race condition between your deconstruction and the bots