Unfortunately there's not much I can really do about that, you're correct that it's happening when you shoot to build but a bot gets there first.
I still want people to be able to construct things that have a bot on the way, because the bot could be far away or the player wants to get rid of some of the stuff in their inventory, etc.
There's no way to tell what bot is on the way without doing some heavy entity polling, and I don't think it's worth dragging the performance of the whole mod down by trying to fix something this small.
Luckily the shotgun can pick up ground items in the vacuum mode, or I'm pretty sure any items dropped by the mod's failsafes are marked for deconstruction so bots can come clean up afterward.