Probably hasn't been noticed by many people since it's less likely you'd be sitting at Sage's table if you weren't in a relationship with her, but the ultimate implication is if you're playing a Jill only path, and you happened to arbitrarily choose Sage's table over the M&J table (being in a relationship with neither of them), you actually miss a Jill scene. Definitely a bug.
Still, it doesn't break the game. You miss the opportunity to lose some Jill points (by perving on her), and you don't get to choose which songs she should go with in her concert, but that's it. No other ominous flags are set (or not set).
On a related note, hopefully the Jill / MC duet is in the making for ep7; that'd be nice (I'm talking the musical duet... the other duet is long over due too

)