1."PHANTOM PUPPET": first there is the "Phantom Puppet" who is not actually the Marionette wich gets proven by not only it being the only canon Marionette who does not have Marionette in its name but also because we actually DO see the unharmed Marionette roaming Fazbear's Fright even if it does not attack Mike during the nights.
And FNAF 6 proves this again anyways since L.E.F.T.E. captures the Marionette and traps it in itself wich would not be doable if the actual Marionette was a phantom.
NOW the name "Phantom Puppet" makes a alot more sense cus the Character is normally always called Marionette since that's its name however the Phantom Puppet is like its name says a LITERAL Puppet somehow created by the Marionette to make Mike think its a Phantom so that it can stay low.
NOTE: I'm not saying there were two Marionettes made for the Freddy/Fredbear locations that look the exact same and that both are hunted by dead kids what the Phantom Puppet is is most likely a trick by the actual Marionette to make Mike think it is a Phantom now aswell
2.PHANTOM BONNIE:
Bonnie still has to be present by FNAF 3 for him to be freed when Happiest Day comes around and he would have to be a Phantom like the other Original Animatronics since Wiliam also destroyed him in the exact same way with his trusty axe.
So where is Phantom Bonnie ?.......
3.THE TOYS:
So.... at the end of FNAF 2 the newspapers say the Toy Animatronics are getting scrapped but in FNAF 3 we clearly see that they have not been scrapped but rather dismantled and them getting dismantled did not free the souls but instead made them Phantoms just like when the originals were dismantled by Wiliam even if the Toys were dismantled nicely and not with violence however that means that means that Phantom Toy Freddy, Phantom Toy Bonnie, Phantom Toy Chica exist but then the question of the day is where are they ?......

You have reached the end of this sorta-long post...
Thanks for taking the time to read this and feel free to respond to these FNAF 3 mysterys with your theorys in the comments below.