Twenty-One Is the Loneliest Number - S6-E7
Corrected entry: Rory is talking to Logan at her birthday party about how the reverend talked to her about her virginity being a gift. She says that Logan's got that gift now, but that's not true - she lost her virginity to Dean, not to Logan.
Correction: If Rory for some reason wanted Logan to think he was her first boy she made love to even though it's not true, it isn't a mistake, it's a character choice.
littlestar
I would believe it to be the character misspeaking in the craziness of the story (because surely that is what the reverend believed to be true), but I doubt that Rory was lying to Logan about being a virgin when they met - especially given that Logan actually met Dean the night of the breakup.