I fairly often experience that some area not covered by miners, lamps or belts are getting marked for deconstruction. Yes, they are pretty close by, and I've started being wary of it, demarking them right after.

Is the deconstruct area larger than the blueprint placed by your tool, for some reason?

Concrete example:
I marked an entire iron patch, with lamps, medium power poles and arrow up. The resulting BP placed the right side belts 2 cells from my rail, so the rail did not have to be deconstructed for it to fit. Could it be, that it tries to place miners on both sides of the belt, thus deconstructing the rail for that?

Yes, the deconstruct zone extends some distance outside the green rectangle. For hardcoded layouts its around the range of the selected miner, for blueprints its half the width/height of the blueprint. It hasn't been changed since version 1.0.0 and was the simplest solution at the time. Will keep in mind on how to improve it.
I did add a "No deconstruct" option that doesn't mark existing entities for deconstruction. Have you tried using that?

Aha! That will probably do the trick! Shame on me for not checking that. Thanks!