I just watched the Waco on Netflix. It was surprisingly even handed and didn't paint the ATF or FBI in a very good light.
I think the problem, and we still see this today, is that the government just decides to curb stomp certain people for breaking the law. Then when things go south, they blame all of their poor decisions on the criminal suspect. "I wouldn't have had to kill all these people if you hadn't broke the law and brought me out here in the first place."
The original ATF raid was meant to be a display of force when they could have just as easily scooped Koresh up the next time he came into town to buy groceries- they had an informant literally in his house who snuck off right before the raid started.
Then, it seemed like the FBI's hostage rescue team was constantly undermining the negotiation team. They interviewed the lead negotiator, and he was basically pushed off the case because he kept butting heads with the tactical guys, and after he left not a single person walked out of the compound before they burnt it down.
Apparently there was quite the discussion on usenet in the late 90s, about all the crazy stuff that happened during Clinton's 2 terms. A blogger I read, Billy Beck, was part of it, and has talked about it off and on over the years. Apparently it was quite... caustic.
Billy Beck is the one that in 2009 coined the phrase, "All politics in this country now is just dress rehearsal for civil war," which you see on the mast head of many blogger web sites.