I'm just wondering if this is something I need to report/make a ticket for... Earlier today I received the High Rarity Achievement when I got a R99 item from the free shop. Just now I hit the next tier for the Subeautique Shopper from getting a Subeautique item also from the free shop.

Should these achievements be counting? I wouldn't think it would since it's the free shop and I'm not technically buying the items?

I think you are buying the items, even if the cost is zero. I know I had my discount card active when I got these Achievements, so I paid less than some people might have.

they are valid achievements. You got them from main shops, even if it is the free shop, and so everything adds up and you get the achievements associated to it. I myself got the r99 achievement from the free shop a couple years ago :)