On a night Phils prospect Jerad Eickhoff impressed with six shutout innings in his Major League debut, Flores struggled to keep the ball down in the zone.
The right-hander, rated Miami's No. 6 prospect by MLBPipeline.com, induced just one groundout. He did strike out five, but allowed seven hits and had a number of well-struck balls find his outfielders.
"He was up all night, really a lot of flyball outs early," manager Dan Jennings said. "Eventually they found holes. He just couldn't get the ball down to the bottom of the strike zone. Elevated the ball. Not typical of what we've seen from him. He's usually been a guy who will work downhill. He couldn't get down there."
In the final weeks of this season, the Marlins will be evaluating a number of their young pitchers. Flores, acquired from the Giants in December for Casey McGehee, has a chance to compete for a rotation spot in 2016.
Flores showed plenty of promise in the Minor Leagues, starting off at Double-A Jacksonville, where he had a 2.06 ERA in 56 2/3 innings. He also logged 58 2/3 innings at Triple-A New Orleans, with a 2.61 ERA.
Prior to Friday night, he made six big league relief appearances, including recording one out on Tuesday at Milwaukee. That lone out earned him his first big league win.
"I just went out there and tried my best," Flores said. "Like every day, I went out there expecting to do well. My pitches, they weren't finishing in the location I wanted them to. I was trying to go low, but stuff like that happens."
The game turned on Flores in the fourth inning, when the Phillies sent nine to the plate and scored four runs.
Flores had a chance to minimize damage, but with two outs, he intentionally walked Cameron Rupp to bring up Eickhoff. After striking out in the third inning, the rookie slapped a two-run single to left, breaking open a four-run lead.
Flores actually felt he executed a decent pitch, but Eickhoff was able to deliver the hit that put Miami in a big hole.
"I was able to locate it down in the zone, but the pitcher got a good swing on it," Flores said. "I just got a bad break off of it. You just have got to rebound from that."