Yeah, all the USS events and related missions are broken in my opinion. If you take a USS mission to salvage a black box, you will keep finding an unlimited number of black boxes until you bring one back, somehow it doesn't matter to the mission givers which one you bring. So you can't even fail that mission (e.g., mess up the scoop) unless you run out of time. And despite this, someone always finds you in the vastness of space and guesses that you are looking for a black box because you “knew to come to this place” – what place, the system? The black box isn't even in the same USS as the branch offer, if it was then at least you could fight the other guy for it.
And branching in general? Why the heck would you ever want to take the branch? The payment is usually almost exactly the same (or even lower), and for some missions you get a fine for taking the branch. Given that you picked the mission from a specific faction, it is exceedingly unlikely that you want to take the rep loss with that faction. So if your mission does not involve USS, then you should never go to a USS while on a mission, as it can only make things worse (if you are offered a branch and don't take it, then you still lose rep with the alternate faction by completing the original mission, just because you'd heard about the offer).
And USS in general? Pointless random encounters. Almost none of them make any sense – ships just sitting around in normal space doing non-sensical things (e.g., convoy flying at a speed that would take years to reach a station, and they're not even going towards one), or pirates and cops hanging around together until you show up and then they both suddenly start paying attention (mostly to you). Or those traders who want one specific thing but won't say what it is except in riddles, and give you no way of returning to them with the item, so either you always fly around with that item using your out-of-game knowledge that you have a certain chance of that same random encounter anywhere in the galaxy, or you get lucky to have it at that time (and not needing it for resource gathering mission, because the trader magically teleports it out of your hold).
I think almost all of the USS and mission branch related stuff should be scrapped and reinvented. For example, a salvage mission should put a marker on your nav and you'd go to that specific place, and there could be challenges there (e.g., cops investigating, others scooping the cargo, pirate ambush) and there should be a realistic chance to fail that mission. The branch offers could come either at that location, or someone could follow you in supercruise and offer the branch there (before or after you've taken the cargo). Meanwhile USS should be events in various stages of progress so that it would be a little less like Truman Show where every NPC is an extra waiting for you to show up before they get in character, e.g., pirates and cops/traders could be already fighting at the USS. (And overall I think USS should be a lot less common to see, not something that pops up all the time.)