After plugging of the anilox cell, scoring of the anilox surface has to be the most common issue that all printers have with their anilox rolls. Unlike plugged cells however, which can be cleaned and in so doing regain their volume, a score line in the surface of an anilox cannot be removed and in effect requires the roll to be reworked.
With this said, it is therefore paramount that everything possible must be done to reduce the possibility of scoring the engraved surface of your anilox. Notice I said "reduce the possibility", this is because a great deal of scoring comes from contamination within your ink or coating. Even if you have filters and rare earth magnets in your ink lines, it is difficult if not impossible to remove all metal, pigment/resin clumping and paper dust particles all of which can and do get trapped between the anilox and doctor blade. This will drag the particle around the surface of the roll, which can and will cause score lines of varying degrees. The irony is that you do not have to dig a groove into the surface coating to have it show up on your print, just dragging a hard particle across the surface of the anilox will change its surface characteristic, which in turn will be reflected in a different color density in the form of a light or dark line.
Doctor blade pressure and angle are also very critical. Too much pressure and too acute an angle will cause the blade to begin to wipe from the back of the blade, which increases its surface area, compounding the issue of potential scoring of contamination digging into the roll surface. You need to make sure that the blade is parallel to the anilox surface at set up, that there is no dried ink on its edge, and that the roll is inked up adequately before the blade is presented to the roll.
Too much pressure on the doctor blade, particularly plastic blades, can lead to the blade softening, which can trap hardened particles in it that, in turn, can and will lead to scoring of the roll surface. I strongly recommend that on receipt of your newly engraved anilox that you wash it thoroughly to help remove any remaining ceramic particles, and that if you chip the edge of the roll you fill it immediately to help reduce further ceramic particles getting into the ink and again getting dragged around the surface of the roll.
Remember ceramic is inert, cannot be pulled out with magnets and is very difficult to filter out, and other than diamond can cause dramatic damage to the engraved surface of your roll. So, as you can see, there are a lot of potential causes of scoring and while difficult to eliminate can be significantly reduced with a better understanding of its root causes.