Father Paul explained it in the show itself:
In the first episode (Genesis), he says that he couldn't find the right one:
Bev Keane: Can I ask you something?
Forgive me, I don’t mean to… It’s just you’re wearing a gold chasuble today. Isn’t that for feast days and special… Shouldn’t it be green today? We’re in Ordinary Time. It’s the seventh Sunday of Ordinary Time.
Father Paul: No, I’m afraid I wasn’t able to locate the green chasuble this morning. Perhaps Monsignor Pruitt, he stored it somewhere unusual given his mental state before he left.
But in the last episode (Revelation), when Father Frank reveals that he is in fact de-aged Monsignor Pruitt, he explains that it was done on purpose:
Erin: You weren’t sick when you got here. You weren’t confused. You knew exactly where everything was in that sacristy. he green vestments were right where they always were.
Father Paul / Monsignor Pruitt: (small smile, almost proud) That’s right.
Erin: You wore gold on purpose. That first Mass. Gold instead of green.
Father Paul / Monsignor Pruitt: Gold is the color of resurrection. Gold is the color of Easter.
Gold is the color worn when we celebrate… a rebirth. I had been reborn, Erin. In that cave. I had seen the angel. I had drunk from the cup. And I wanted everyone to see it on me the moment I stepped out there. I wanted them to feel it before they even understood what they were feeling. It wasn’t a mistake. It was a declaration.
So as you can see, Frank/Pruitt werewore the vestment that is usually woreworn on Easter, celebrating the rebirth of Christ, because just like Jesus, Frank was celebrating his own rebirth and, in his mind, the rebirth of the Church that the "angel" will bring with him to the community.