That's just baseball, according to utility man Marwin Gonzalez.
"It was just one of those games," Gonzalez said. "We're not going to score 10 runs every game. We're going to miss pitches. That's baseball, I guess. Like I said, the offense isn't going to be there every single day. Today was one of those days."
Center fielder George Springer flied out to short center field on the first pitch of his bases-loaded at-bat to end the second inning.
In the fourth, Jose Altuve grounded out to third to end a threat, and first baseman Yuli Gurriel grounded into a forceout at second base to end the seventh.
Gurriel extended the Astros' doubles streak with a run-scoring two-base hit in the second and Altuve added a solo homer in the third, but Houston left 10-plus men on base for the second consecutive game.
The Astros stranded 10 on Friday and 11 on Saturday, tying their third- and fourth-most left on base in a single game this season.
"Obviously, Springer got the popup and Altuve with the groundout -- we worked really hard to get into those situations, just didn't come through with the hit," said manager A.J. Hinch. "Credit to them, we obviously had our opportunities. We had every chance to break things open a little, or at least make things a little bit closer, but they won the big at-bats."
Houston scored both its runs off Minnesota starter Ervin Santana, who is now 4-0 in six starts against the Astros. For the night, Houston went 7-for-33 against four Minnesota pitchers and drew six walks.
"[Santana] is trying to [get] us out," Gonzalez said. "We're not facing a pitching machine, you know? He did good today. He threw a good game. And he's one of the best pitchers in the league."
Christian Boutwell is a reporter for MLB.com based in Houston.