That's because Yi's AP ratio's on Meditate are insane.
Not only does he gain an enormous amount of armor and MR at all levels (100-300), but he gains an enormous amount of health regeneration (that scales with AP at 3.6), and heals at the beginning and end of the ability (that scales with AP at 4.0).
So yea, he became invincible. Your only real hope would be if you were an auto-attacker that was using Last Whisper and Black Cleaver with ignite.
Also, those that think Grievous Wounds or Ignite is a counter to AP Yi's regeneration is exceptionally false. Even at 50% reduced healing, he will still gain more health than you can deal damage. If you don't have hard CC, Yi is invincible during Meditate. I think that is the point of the ability, to allow a very squishy AP/AD carry to time the ability and absorb a lot of punishment in order to continue doing their job. It's kind of a reverse-CC. He is unable to stun, slow, or root, but he can force a team to blow CC on him.
Which brings me to my next point - Yi is a walking AD Steroid. Why does no one ever build him as a bruiser?