Bit of an edge case but may be causing a secondary crash with another mod (https://mods.factorio.com/mod/newly-constructed-machines-wait-for-their-modules/discussion/6755dea00e31cbb37ea7ca2d) - if a machine is marked for deconstruction and any other machine ghost is placed on top of it, requesting a single module change on one machine will additionally request the same change in all machines overlaid with that one, regardless of whether the other machines are in the selection box. This only occurs with changing a single module (right click), and not filling all slots with one type (left click), which will only request modules for the correct machine.

Thanks for the report. For 'insert single' mode, I iterate over each selected machine, and for each I create a hidden upgrade planner then apply it to that machine using surface.upgrade_area{area = entity.bounding_box, ...}. I guess I hadn't considered the fact that there might be overlapping entities... so I guess if 2 entities are completely overlapping then they'll each get their custom upgrade planner applied to each other and there's not much I can do about that.

I could change it so that I restrict the bounding_box I'm using to the outer-limits of the player-selected box - that way at least it won't apply to entities that were outside of what the player selected. I don't think I can fix the case where the 2 entities completely overlap though. Would this at least be helpful?

In the case of two entities perfectly overlapping it's probably better to have them both be affected, otherwise one would be inaccessible 😅
Ran into the issue when trying to move a large factory one tile to the left and bots were slow about it, greatly appreciate you fixing it :)