So I had enough IP to buy a Tier 3 rune of Magic Pen, when I realized it said the cost of that rune was 0. I knew it wasn't true, so I went through all the runes in the third tier to see which ones also said they cost 0. However, I accidentally bought a rune I didn't want while testing this bug, which is why in the pictures, I drop from mid 400 IP to 13 -_-. Anyway, as I was going through the runes, I noticed a pattern, to the point that I ended up not having to go through every single rune to pick them out, I knew before I even looked which ones would say they cost nothing and which ones didn't. Any rune (Mark, Seal, Glyph, or Quint) that has flat Magic Resist, flat Magic Penetration (this includes Marks and Quints of flat HYBRID penetration), and flat Ability Power have this bug. Only these perks seem to be buggy, doesn't matter what type of rune they are. Also, I went in to the other tiers, and saw the same thing occur.
Also, these runes are NOT free. The calculator is just wrong. So don't do what I did and buy the wrong runes on accident.
Edit: Can you guys check out my other report? I REALLY want this to be fixed, so comment on it there to get RIOT to notice it.