That has happened before - you could have a "grand slam single" like the one Robin Ventura hit for the Mets in the 1999 NLCS.
With the bases loaded and the score tied at 3 in the bottom of the 15th inning, Ventura hit the ball over the fence for an apparent game-winning grand slam. But his teammates mobbed him before he could reach second base and finish rounding the bases. Therefore the official scorer ruled that Ventura would only get credit for a single and that only one run would score on the play. Final score would read 4-3 instead of 7-3. Made for some unhappy people in Vegas that day.
Wikipedia article on the "Grand Slam Single"