There are repeatable techs, like optimisation, augmentation, etc. They are all quite cheap techs and in theory give you small bonuses, the problem is they don't stack. They either should stack, or they shouldn't be repeatable. So before long your 3 subsidised tech choices are all the broken, repeatable techs, essentially meaning you have to research the other techs at full price, basically reducing your science output by 50/60%.

Never had that happen and I've played the game for almost 1000 hours since Beta.  In my current game I'm generating so many research points that most techs only take 1 or 2 turns.  I still only have 1 of the end of tree techs that you're talking about in my bonus pool.

I watched the video you linked starting at 32:30 for 2 minutes and it makes the point about those techs not stacking, but it certainly doesn't show the bonus section filling up with the end of tree techs.

I will agree that we've all complained that if the end of tree techs don't stack then they shouldn't keep showing up in either the bonus or additional tech research lists once you've researched them.  

I was just able to test Manufacturing Capstone and it does not stack and still came up for a third time in my bonus list.  I'm pretty sure they all do this but if I can confirm with other capstone techs I will post here.