Benson, ranked as Minnesota's No. 5 prospect by MLB.com entering the season, is expected to be out six to eight weeks.
"He had surgery on the hook of the hamate bone," Ryan said. "It had nothing to do with his struggles. He did it just recently."
Benson, 24, began the season at Triple-A Rochester but struggled, as the outfielder hit just .179 with eight extra-base hits in 95 at-bats. He was demoted to Double-A New Britain, but continued to have trouble at the plate, batting just .156 with a homer in 32 at-bats.
It came after he hit .284 with 16 homers, 14 stolen bases and 29 doubles in 114 games at Double-A last year before being called up by the Twins in September. In 21 games with the Twins, Benson hit .239 with six doubles, a triple and two stolen bases.