I have also seen instances where the damage reported by my team (i.e. the report showing the per-character damage, and the total squad damage) does not match the score reported on my guild scoreboard.
I don't know if it's a visual bug, or if the damage the squad does to protection is being added to the "squad damage report", but only damage to Nihilus' health is logged on the scoreboard. Perhaps that would account for the discrepancy?
@EA_HighCommand you guys might open up a new raid in development, attack it with a semi-weak team, and compare numbers between what the squad shows and what the board shows.
EA QV Team