This is pretty easy to reproduce but the specific outcome depends on the particular cliff and location of the roboport - so for the sake of determinism I've included a save (follow the below from 2 for the cliffs north of the player, inside the wooden chests).
- Set up a powered roboport within range of some cliffs; give it 1 construction bot and a storage chest containing cliff explosives.
- alt-D and select a region of cliffs to schedule them for deconstruction.
- While the construction bot is en-route but before it has thrown any explosives, right-click-deconstruct the bot to pick it up.
- alt-D and shift-select the same region of cliffs to cancel the deconstruction.
For the provided save, note that in step 4 one of the cancelled cliffs doesn't get a rectangular selection box, and the number of cancelled cliffs does not match the number from the original deconstruction request in step 2.
There is a trivial workaround: to get rid of the red crosses, select the cliffs with a deconstruction planner again, then cancel the deconstruction order by shift-clicking again.