Jane was upset because her stepfather was abusing her. Holden's reaction was to sit next to her and put his arm around her. But instead of just comforting her, he begins to kiss her all over her face. He confuses lust with sympathy. This could have been one of Holden's first chances at real, not just sexual, intimacy, but Holden is obviously not ready for this. Ironically, he sees the same kind of approach when he witnesses a Yale-looking guy telling a girl about a suicide of a friend while trying to grope her under the table. He's appalled by the guy's behavior but doesn't seem to connect it to his own.
Jane starts crying after her step father yells at her. At first she just sits still at his presence but once he leaves Holden notices a teardrop. He comforts her by kissing her all over her face, and staying with her as she cries out her feelings. Of course this is a sort of intimacy between them, but it looks like it didn't lead to anything in their relationship.