let's say we're talking A2 sights with the theoretical Army zero.
zeroed at 300, lil low at 25. when you flip the sight to the 0-2 ap (0-200 metres) the trajectory drops 4-6MOA (depending on make of ap) bringing the POI into better coincidence at the nearer ranges. You can se by the chart that if you drop the 225 POI (+4") by 4MOA you'll be about 5" LOW-at that range with 1MOA being 2.25" at 225 so -4 MOA would be -9" minus the +4" already present. Additionally if you drop the 100 POI by 4 MOA you're 0.8" low at that range.
Army spec is to use the 0-2 ap for "close range, low light, or moving targets" so that sight is lower to adjust for that range.
that's what I meant by "using the sight as designed."
For duty use you're better off zeroing with the large (0-2) ap and leaving it be. Use of a same plane ap is also an option as is an Aimpoint.