There were very few SBE 3's in the first production cycle that truly had mechanical cause and effect issues shooting high, if your gun is new, newer you MAY have fitting issues. I would suggest looking at a few shotgun fitting video's to gather the concepts and apply them to fitting your gun to you.
I have had 5 SBE 3's from the Performance Shop that were patterned by Rob Roberts, all 5 shot a near perfect 60/40 pattern, verified pattern. I then inserted a 12 gauge laser into each of these guns, the point of aim was perfect on every gun. Another way to work it, all 5 guns shot a pattern exactly where they were pointed.
I would acquaint myself with fitting your shotgun and understanding the role of the adjustment package from Benelli. Your SBE 3 with the center bead should assist you in alignment of fitting.