What ammo are you using?
The Leupold 3x9x40 with the Bushy turret is, if I have been told right, designed specifically for the 250gr/2200fps Hornady load with a BC of .210.
Remington offers a 260/BC .144 @2180 fps and a 275 Barnes/BC .215 @ 2125fps These loads will very likely not agree with the scope calibration values. The true velocity also may be different then claimed on the box.
Ruger makes rifles with both 16" and 20" barrels, AR platform lgts vary even more. Barrel length affects speed.
Last, is your range accurately laid out? Is the 100 yd range really 100yds or is it 100M? maybe it is 10 yds off +/-? did you just pace off your distances or sight in at 50 for a 100yd zero? GIGO