The module is called Red Hand of Doom.
Sorry, yes, you had mentioned that. Tiredness makes me forgetful.
I think a lot of my problems stem from not asking them to choke down plot waypoints.
It shouldn't be something you ask them to do. It should be something they are willing to do because as players they should want to tell the story and find out what happens.
For example, the module did not expect them to go to this city until it was empty and only manned by army units. They escorted the refugees the entire way. The module wasn't really too telling on what to do in that situation. So I improvised.
I remember the section now. In this situation the path of least resistence is probably best. Perhaps the refugees could allowed to pass through and some stragglers from the city escort them to the next nearest place. Or perhaps the army would be grateful to have some civilian help to contain fires, supply fresh arrows...etc.
All I learned is that by giving players freedom I receive pain.
I'm going to go all cynical for a moment, but... welcome to roleplaying. Players never do what you want them to. They don't want to caught in the webs you've spun. Players want an easy time of it for the most part. Slay monsters and take their stuff.
As has been mentioned, the best thing to do before you get jaded is sit everyone down away from the game and talk it out. Find out what they want, and explain what they want. Find a compromise. At least you'll all know where each other stands.
In my naivety I decided to expose them to a situation where it wasn't obvious if it was an enemy. They took freedoms, I allowed it, and tried to expose them to the basic principals outlined in the DMs guide. Sometimes there's a bigger fish, your characters don't know everything, not everything is a loot pinnate.
It's not naivety. You are doing what you need to do as a DM to make a fun and interesting game. You can't help it if your players won't help make it fun and interesting.
But some players don't think their characters can do any wrong. And you get an experience like mine.
I think probably everyone on these forums can step up and say that at some point or other they have had players like that. People are competative even on something that should be a co-operative effort.