Now you're blaming multiple things on the people who created Unity.
Don't you think that it's more likely you're in denial about your own sloppy game code? I don't mean to be rude, but you've done that twice now for two different problems, so you might want to rethink your logic process.
Which goes back to what I said. When you had the "unexplained" problem, by merely blaming someone else for it, you failed to work out why a really basic fuck-up on your part was happening, and because of that you didn't deepen your understanding of the engine, and of course, next time you have a similar issue, you don't delve into the "why" either, but blame some other mystical "Unity Bug" in what is now probably the world's most widely used commerical game engine.
At this point I've built about 40 game demos in Unity ranging from Tic Tac toe up to including some seriously complex shit, each time there were bugs, every time it was my code and not "Unity Bugs". Your code is junior-level. There's no way it's not the cause of your own bugs. Again, I'm not trying to be rude here, but you need a reality check, and I'm not going to spend time helping people who keep blaming the tools rather than improve by taking the time to work out why things are happening.
Unity is after all, a general purpose engine. You can make any existing or even hypothetical type of game inside Unity. Therefore Unity can't know what's "right" for your game. It only follows the code you typed in, which can be the code for any hypothetical game genre that could exist. So Unity has no way of going "oops, I didn't draw the selection box on that unit" because Unity has no built-in concept for "Unit" or "Selection Box" or any idea when you might want the selection box or not want the selection box. It's your code's job to create these things and wire them up so that they behave like you think your RTS "should" behave. Unity only reads the code you typed, it has no knowledge of your "authors intent". If the selection box on a unit disappears when you didn't want it to, that's because somewhere your code said for that to happen, at least in 99.99% of cases: Unity was just following the written instructions.