I doubt that Father Phil drove around with a communion kit to a clothing drive and then to Carmella on the off-chance that they have Communion for some reason and a sip of wine will get her in the mood. They drink wine anyway before that scene and do so casually, since Father Phil feels at home there and usually passive-aggressively helps himself to their amenities. He doesn't need to trick her like that.
So I think he was telling the truth, and the options as I see them are:
- This is a goof and the writers\production simply didn't think this through;
- The patient Father Phil was visiting either died or got better before he got there, so his services weren't needed after all;
- Father Phil refilled the decanter somehow. Maybe he has some extra sacramental wine in his car for emergencies. This is conjecture, though.