Charlie Austin gave the hosts the lead with his 26th goal of the season before half-time substitute Cywka struck with six minutes remaining.
While the goal prevented the Tykes from losing three consecutive games they still dropped into the relegation zone after Wolves' 2-0 win at Millwall.
As such, Flitcroft believes it was a case of two points lost.
"I'm not happy with the point, I came for all three," he said. "We wanted all three and we needed all three.
"With regards to the second-half dominance we had, I felt as though we had to chase the game but some of the play in the second half is what I wanted to represent one of my teams.
"Tomasz Cywka's work ethic has been incredible. The guy has been out of the team and he's been someone who has kept patience, been resilient and has epitomised everything I believe a human being should be.
"I was disappointed in myself because of maybe the way we set the team up in the first half. Chris O'Grady led the fight second half but he should have been down the middle. Hindsight is a wonderful thing but it is definitely something I'll learn from."