I originally thought in "Change of Heart" sending Newlyweds Worf and Jadzia on a crucial and dangerous mission that resulted in Worf choosing his wife over the mission. But I went back and watched the episode and it was Kira who gave them the orders. So that was her worst command decision.
AR-558 was a complete botch job from the top down, especially because Starfleet lost the array anyways. While Sisko wasn't the one sending troops to their deaths, that decision came from above him. Getting into a ground battle with Jem'hadar being significantly outnumbered in bad terrain was just stupid (again, not his fault).
Instead of trying to hold the communications array, Starfleet should have just destroyed AR-558 and the array instead of squandering lives fighting over some rock.
Monitoring communications that the Dominion made didn't stop the Breen from developing their dampening weapon and the ultimate destruction of the Defiant and many other ships in the process of losing Chin'toka back to the Dominion anyways.
As far as individual decisions, Sisko's Gamma Quadrant tactics were questionable, which speaks more to how well the Founders were prepared than it does to his military expertise, because he was usually on the right side of strategy in the Alpha Quadrant.
All in all, in "The Adversary" Sisko trusting Krajensky and not confirming his orders with Starfleet before sending the Defiant right at the Tzenkethi for no real good reason (other than to make Federation presence known to them) was a poor decision.
Yes, Sisko had no way of knowing that Krajensky was a Changeling, but he played right into the Founders hands and needed Odo to bail him out by killing that Changeling.
His actions in that episode called for a mutiny but no one had the balls to pull out a phaser and end his command.
