For one, this does not belong in the bugs section. General yes most likely.
Two: From what I've read, you have a bad habit of drip feeding, or flat out not giving, critical info that makes bug hunting nearly impossible. This isn't Twitter: You can type up responses larger than 140 characters. And we ask for you mod list, system specs and the error or log because it helps us find and hopefully squash the bugs. And please give specifics! The more specific you are, the easier it is for us to help you.
As for your "bug" it seems like you got in a fight with the heg, maybe even a retreat fight, went somewhere else, had an encounter with another heg fleet while your transponder was off, they demanded for you to turn it on, you did and they noticed that you recently "attacked" one of their fleets.
A tip: The outer boarder will pulse this orangish red if you've done something to anger a faction with your transponder off and turning it on would reveal who you are.
Maybe the game does need a warning in dialogue if you are talking to someone and turning on your transponder would reveal your evil deeds