Block Groups from Connected vehicles activate for both vehicles if the name is the same.
When two vehicles have block groups with the same name, activating it in one vehicle will activate it for another vehicle. For example, if using the block group "Ion Thrusters," for small ship A and large ship B, when the small ship tries to dark with the large ship, turning off the Ion Thrusters to avoid damaging blocks will turn off the Ion Thrusters for the whole ship, as well as a potential small ship C, D, etc. that is also connected to the same ship.
The workaround I use is to add a tag to each block group, for example, "Ion Thrusters - Ship A," "Ion Thrusters - Ship B," etc. But this can be quite tedious, as for every small ship bound to the large ship, it needs to be completely reprogrammed, as any attempt to rename a block group creates a new block group that must be reassigned in the toolbar, while manually deleting all of the old block groups. This also adds unneeded clutter to the necessity of tagging every block group with a unique tag for any ship intended for docking, or to accept docking ships, and also necessitates creating a database of used tags to avoid a potential use of the same name between two ships, which is harder to control in multiplayer scenarios.