It's malnutrition plus exhaustion, like, long term stuff. And there's some burn marks on his hand...

[Junpei was completely at a loss. Minato recognized him, so it wasn't before they met... He hoped.]

I can't remember any time I was with Minako that shit got that bad to be starved; so I dunno how'd he be like that, if things were the same for him and 'another' me. I'm totally in the dark on this...