They actually addressed that in one of the IDW comics and it comes up quite often in stories with that premise. Usually there's a hand wave that she catches up with her studies when she stays with her parents.
Side note: The "ask mama Twilight" tumblr comic blog was incredibly wholesome and a little tear jerking. Worth a read.
You're not talking about issue 40, are you? Where Celestia turns Twilight into basically a full-time nanny for baby Spike, and it goes about as well as that usually does in real life (with Twilight nearly flunking out)?
And then at the end, just as Twilight realizes that Celestia intended for Spike to be her first friend. Not only did Celestia have no grasp of the struggles of underage mothers, she somehow thought that a baby is an appropriate substitute for making friends one's own age. No wonder Twilight's social skills are still crap when the series begins.