Mechanical Offset is something you need to be familiar with. It's a fact of life with straight line stocks (like on your AR).
What that means it that the line of sight on your sighting system, be it irons or optics, sits above your line of bore. This means the line of bore is actually pointing in an upward angle and your bullet will intersect your line of sight at your zero distance. The round will then continue it's upward trajectory until it hits it's apogee, the round will then start to fall and eventually cross your line of sight again. With a 50 yard zero, which I highly recommend, this means your round will cross at approximately 200 yards.
What does all this mean for you? With a 50 yard zero at anything closer than 50 yards your rounds will hit low if you hold your "normal" zero. At 25 yards you will hit about 3/4-1" or so low. At 10 yards you will be about 1 1/2-2" low. At 5 yards you will be about 2 1/2" low. This is all dependent on optic, mount height, etc. What you need to do is learn your hold-overs. Do this by holding your dot on a spot on the target and seeing how low your impact point is. You will then need to hold that much higher to achieve a hit on your target. Even if you continue to use a 25 yard zero you will still need to take mechanical offset into account as you have already discovered. Also a zero closer than 50 yards has fairly dramatic effects at longer ranges as well. IE: a 25 yard zero will hit about 6-7" high at 100 yards...again dependent on ammo, optic, mount height etc.
Your best bet is to get to a basic carbine course that covers this and run the drills that demonstrate the issue. This picture will help illustrate what I have spelled out above.
aimpoint zero.jpg
As I mentioned, different zero distances will have different effects on mechanical offset as illustrated below.
aimpoint various zeros.jpg
PS: Full Disclosure...I work for Aimpoint as a Prostaff member.
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