Number one isn't game breaking by any stretch, but it seems like anything already inside the box is marked for deconstruction, regardless of what it is, and since I have a giant base full of concrete, it marks my concrete for deconstruction if the ore field is on top of it.

Number 2 is unfortunately game breaking, if you accidentally mark a patch of Crude Oil it'll send you to the main menu with this error message: http://imgur.com/a/Ixe4r

I can confirm both issues, let me see what i can do

I've uploaded an updated version that:
a) fixes the issue with the oil field
b) adds a checkbox to disable deconstruction

There is unfortunatly no API that allows to filter what is deconstructed.

Both fixes work excellent, cheers!

And it even handles ores added by mods, kudos.

There is another issue:

When I create a plan next to other entities, the entities will not be deconstructed, if they are outside of the selection box. However mines get blueprinted in a way that their centre is inside of the selection box, but since the mine is 3x3, some tiles can be placed outside of the selection box.

So sometimes ghost-mines are placed and overlap with existing entities directly next to the selection box.

kobold-der: Thanks. I am tracking the issue here https://github.com/masterpoi/MinerPlanner/issues/6