Wow. Awesome work, XRizerX. Seems a bit random that inventory would cause that to happen, but.. nevertheless, clever solution. That's exactly what my playthroughs were like. My second run was a full achievement run... and my first one I got whatever came naturally.
On my second playthrough neither the Shoe nor the chinpokomon next to the crab person in the sewers spawned. They are the only things I need for my remaining two achievements. Please patch this.
Playing on PC/Steam.
I've just made it to the end, and I can confirm the shoe didn't spawn for me, either. So I had two that did not show up on my second play-through. It's also a bit silly that it locks you out of the friend achievement as well, because of this.