Typically you want at least 6inches clearance between the bed rails and the trailer overhang to allow for some shifting as you go over rough roads (particularly in campgrounds where sites may not be even and level).
Newer trucks sit higher and particularly if you match it to an older trailer, this can cause problems.
The most common solution is to "flip the axles". Basically this means rather than mounting the axle above the leaf springs, you re-mount them below the leaf springs. This gains you 4-5 inches of height on the trailer.
You may need to adjust the hitch and pin box height but the trailer should still remain level, so it's often not a solution by itself.