As you know this is due to a driver controlling the junction. It could be that you have a consist too close to the junction causing the points to be locked. The other issue is a driver heading down that particular route has locked the junction a head of time.
There are a couple of ways to solve each issue.
For the consist that's two close, you can extend the siding a bit and move the consist away from the junction. The distance is 20 meters, or 2 squares in grid view.
The alternative is to click on the tab for track marks (yes that one). Pick adjust trigger radius, and adjust the radius for the junction to something smaller. This is a common practice for yards where you want the consists to be a bit closer to the points.
For the driver somewhere else, you need to put signals in between. What kind is determined by the layout of your route.