In "In the Pale Moonlight," when Sisko orders Bashir to prepare biomemetic gel, Bashir responds that he'd like that order in writing, and Sisko complies. Two questions about that:
1. In the real life militaries of today, can a subordinate demand of a superior officer that they put an order in writing if they feel that the order is to do something questionable?
2. What good does it do to have an order "in writing" when "in writing" means "electronically on a PADD"? Is there anything to keep that electronic copy from mysteriously being deleted next time Starfleet starts asking questions?
I can't speak for Bashir or Starfleet, but I work as a train guard in Sydney and as such safety is very important. If I'm ever told to do something that I think is unsafe - "Sure, you can go into the rail corridor without the correct PPE!" - then I'll ask for the order in writing. And then I still won't do it. And when I'm asked by the big bosses why I didn't, I can say, "Look what they want me to do! It's signed and dated!"
Personally, I think Bashir was just calling Sisko's bluff. Most people wouldn't want such a paper trail left after asking someone else to do something illegal like that. he didn't realise that Sisko wasn't bluffing. I know if I was ever in that situation, the person giving me the order would back down if I asked for it in writing, because they knew that a formal complaint was going to come of it.