Yeah, this part confused me as well. If you take the Prequel comics as canon, then Eggman found the phantom ruby in front of his doorstep one day, but I guess decided to make more of them because they're super cool shit. His attempts to make others ended up being just failed 'Prototypes' that weren't nearly as hot shit as the real deal, so he just shoved the real thing into Infinite. That's my take, anyway. At least the comic implies that it's most probably the same ruby from Mania to begin with. For me, Sonic Team not even bothering to put Green Hill on South Island anymore (unless the whole game, city an' all is actually on one fukken huge South Island? I guess if you wanted to explain the Animal-only population, but that would involve taking the game's world map with a pinch of salt.), and no epilogue explaining what the funk happened to Infinite and Eggman are some of more annoying story offenders for me. Also, I swear Forces contradicts itself regarding the Phantom Ruby powers, on top of contradicting Mania. All in all it's best to think about as much as Sonic Team did: Not at all.