There has been some excellent points brought up about this problem area. It's also a good subject for the obsessive type, so I lke it a lot.
I have a had this problem and it aint fun. In my opinion it is a number of small errors that add up. That's why all of the above tips are good. But, I believe there is one or two that has not been mentioned.
The big one is hard to describe without a chalk board to exaggerate and make my point. Notice the picture below.
The file guide is clamped onto the ricasso pretty snug, naturally, to hold steady for the filing of the shoulders. It has guid pins and screws to close it and to keep things lined up. Right? Well, yes, but here is the problem. The guid pins can only help. The object it's clamped to must be parallel to make the thing work right. If not the upper flats where the file rides are no longer parallel with each other , because the guide pins can only do so much and then they flex when the guide is clamped against the ricasso. This does one of two things. It ridges up at the blade or it valleys at the blade. Now when you start filing, changing directions of the cut, you get differences in elevation on your cuts. That is one obvious problem that can be fixed by checking the ricasso and work it toward parallel as you finish. Karl does an excellent job of this as he has described his method here before.
Another thing is the way we use our files. I'm right handed so I favor using a particular side, or to be more exact, a particular corner of the file. This corner gets more use whether I am hogging and whether I have it flipped over. The other two corners are relatively fresh and sharp. I have long since started hogging the prefered direction, getting it as close as I can, then turning everything around where I can access things with the other file corners and give the last few strokes from that direction. I usually can feel some more material being removed when I do this. I then check it to see that the shoulder is flush by dragging my finger nail or the file tang across the area being filed to see if it's flush. If not, I get another file or make more strokes or something.
I believe Karl files the top and bottom and not the sides making the guard slot very tight on the sides for his. That is great, but I dont have the precise milling capabilities so I file the sides too.
This is another thing that will give you gray hairs. Filing the sides. When filing the sides, you have to go deep enough to get past the dullness of your file. In other words, your file. although cutting good, is not as crisp as you think it is in the corner, for a variety of reasons. Number one being that we are not machines and cant make perfect strokes without concentrating. Concentrate! But, the corners of the file always leaves a tiny little "round" in the juncture of the two planes. The quality of the file, the newness of the file, and how we concentrate, all will affect this corner. But, back to the point. Go deep enough to where the "round" corner of the file becomes flat again. This is not much, but you have to get there or you wont ever get a good fit.
My side depth is about .005-.006 deep. This requires me to then work on the guard slot to settle it on in and to fit up tight and not wiggle. I actually round the rim of my slot when I see the shiny contact points that are interfering with the fit. All of the work, naturally, has to be within the covering of the ricasso. Were talking tiny amounts.
I had to really emmerse myself in the details to get it to fit good. But it works for me.