I haven't seen this movie, but based on the snippet you quoted, it seems pretty obvious that Holly and Messer are dancing around the idea of being in a relationship. I'm assuming this obsession with "planning" is a new development, to Janine as well as to both of them.
Holly's assumptions about Messer's "plans" are stereotypical of how "men think about sex." ie: They get what they want and then they leave ("with no plan at all" / "It never occurred to me that you had any interest in my plans") She's using "plans" as a metaphor for "relationship."
Messer was expressing his interest in a continued relationship ("I kind of had a plan in mind") and then saying he's not as experienced with long-term relationships - so he has been known to enjoy the single life in the past, but with Holly he's interested in something more.
Janine picked up on the metaphor that they were saying "planning" when they meant "relationship" (ie: a "plan" for living together) and inferred that if these two previously single people were suddenly "planning" together, they probably had sex recently.
PS: I'm assuming there were also some soulful gazes and dramatic pauses between Holly and Messer during this conversation that would have further emphasized the double-entendre for Janine.