Flaherty (9-2) left after two-plus innings in Tuesday's 4-3 loss to the Detroit Tigers. He allowed four runs on four hits with three walks on 46 pitches, with his velocity dropping dramatically after the first inning.
"It's an accurate description," Flaherty said of his shoulder assessment after Tuesday's loss. "... I'm just frustrated for the most part. It was tight, just tight. It wasn't normal. It got less comfortable as the game went on. I'm just ticked off."
Shildt told reporters on Wednesday that the result of an MRI was "mostly negative" with no major structural damage appearing in the scan.
The 25-year-old starter missed 60 games (June 1-Aug. 12) with a left oblique strain. He had given up just two runs in 12 innings covering two starts since he returned after being activated from the injured list.
"He didn't feel good toward the front of his shoulder. We went out and checked on him," Shildt said Tuesday night. "He said he was sore. I felt good taking the ball from him. It's clearly concerning. ... There's some concern when your ace has to go down."
The Associated Press contributed to this report.