Has an NCAA Baseball game ever ended 31-16?
Exactly once. On February 14, 1999, Creighton beat Air Force 31-16, and no NCAA Baseball game before or since has ended that way. When it happened it was a scorigami, the first 31-16 in league history.
That makes 31-16 the 457th most common final score out of 531 that have ever occurred in NCAA Baseball. One point away, 32-16 has happened never and 31-17 has happened never.