When Sisko slams his hand on the desk in anger, his breaking of the desk's surface glass was unintentional, but they kept it, since it underscored Sisko's frustration at being on the losing end of several engagements.
The episode is dedicated to the memory of Brandon Tartikoff, the former Chairman of Paramount Pictures, who died in August 1997. It was Tartikoff who originally approached Rick Berman about doing a new Star Trek series, and it was Tartikoff's idea to do a stationary show, as opposed to one on a starship.
The opening shot of "A Time to Stand", featuring the retreating flotilla of Starfleet vessels, was one of the last mass scenes entirely composed of footage of physical studio models, save for the CGI USS Defiant. To beef out the scene, the production staff built several new ships, kitbashing them out of parts from commercially available AMT/Ertl and Revell-Monogram Star Trek model kits.
This episode has one of the longest teasers in Star Trek, lasting just over seven minutes.