this is a big problem in sniper mission with 500+ range. Sometimes the enemys complete disappears in the terrain.

Maybe they're behind grass and the grass texture doesn't load?

This gets worse under terrain detail set to low. (Although absence of grass compensates for that.) It configures not only presence of grass\another things, but also fidelity level of ground trigonometry.
Seems that when the engine decides it shouldn't draw things in HQ, it simplifies trigonometry in a way that causes it to ignore certain low-altitude points, where, sometimes, you could find a soldier lying prone.
So basically maximum range for high-detail drawing in all detail levels must be increased for this issue to be fixed.

You could also notice that, sometimes, when you see an enemy near some hill and shoot him, bullet doesn't really arrive at him - it arrives in this nearby hill in between which isn't drawn well enough.

Eh, pretty sure this is a feature (to make up for lack of clutter at a distance introduced somewhen around A2/OA, I think), not a bug. But yeah, I've never liked this ugly hack either...

IMHO they should just get rid of it (as with any other feature that was just half-assed, e.g. ponds) and come up with a proper solution once they have one.

I can confirm it with:
Object: high
Terrain: High
Visibility Overall/Object/Shadow: 3096/2000/100

Radeon 6950, latest catalyst, Win 7 x64

The worst case scenario I've whitnessed was with the following configuration in the Adapt campaign - Attention... mission:
http://i17.photobucket.com/albums/b68/Bucic/BI%20Forums/adapt_attention_aiunderground_issue_no93884_107410_2015-06-04_00003_zps3zzmzemz.jpg
Some soldiers in the north-eastern part of the camp literally disappeared under ground when prone.

Please comment, this will make it on the first place. I tell you bad thing. This is not a bug, this is "optimalisation" thing. on Todays PC's this is giving you 3 fps more maximal. Its very useless and it should be in optionf available to disabling. It appear in Arma 2 as well, soon they have added this in Arma 1 (games was runing fine, so i dont know the reason why they do that). Since that time Ai learned how to sink in grass. Actualy they are in grass, but grass is rendered diferent over distance. It look like ground texture, but it isnt - it cover the ground on same heigh, as normal rendered grass is in the place. Likewise this option should be available to disable, so the game can look more natural. BI devs, if you worry about FPS drops, just disable grass animation over distance (made by wind, or object standing on the grass)