Do any of your DB mods touch the NPRs in any way?
In a way, yes, since I've enabled some of the "advanced" techs, changed some stats of components and planetary installations. But they shouldn't impact the NPR default behavior, unless it's an unintended consequence (it happens).
I've edited a copy of the saved DB to take over the NPR just to give alternate orders to the 6 fleets (3 beam bases and 3 missile destroyers) with orders to "Join Operational Group" that would apparently be a "Reinforcement Group". Saving the DB without incrementing time, changing the race back to NPR, and running it again, the error pop-ups didn't appear, so I believe I've identified what the error meant.
I believe this "Reinforcement Group" is a bug. It isn't present in any of the tables that describe NPR operational groups. Maybe it's a leftover from a previous version that was discontinued, or something that isn't fully implemented yet. The vessels were built after the start, and probably received this NPR-only standing order, but it's apparently not functional.
Maybe it can be reproduced on a non-edited DB, starting the game with just one starting NPR (settings are no spawning new NPRs by the NPR), leaving the player race isolated in its system, doing nothing for a *long* time (for me it took 15 years), letting the NPR expand. They'll build more vessels and we can then examine the DB to check if there are fleets with this standing order (48, with NPR operational group 11).
I do note that this NPR has been very successful and built lots of ships, though only these six had a problem. I recovered an old save from just after the time these 3 ships were built, and they already had this order, but apparently they did nothing for a long time, just stayed quiet and alone in their own individual fleets. I don't know what made them try to execute the order so long after they were built (~10 game years earlier), maybe it was meeting my exploration ship in their home system and turning hostile. But if they were created with this order it was already an error waiting to happen, and a mostly useless ship for the NPR who apparently don't know what to do with them.