First off, the tiles scanning people have been talking about it. There is no way to prevent people from using it unless they record their game with Fraps or something, so I think the most fair thing to do is to put everybody on the same page by explaining how it works: it's impossible to move to a tile that's already occupied by another unit, and this also goes for invisible units, so you can use this subtlety to detect them. If you hold the right-click when your selected unit is on the ground, a grid appears over every tile that you unit can move over, which makes it easier to see an occupied tile. But now, if you release the right-click, your selected unit will move wherever you are pointing. To prevent that, you can point back to the tile your selected unit is occupying and release the click there.
Note that this doesn't work against flying invisible units.
Secondly, there are a few major bugs that can occur during the game which can prevent you from using your units correctly:
1) The "dash bug": a blue movement will be considered to be a dash by the game and your unit will hence exhausts their two actions in one move. The only way to see this coming is the "dashing!" sign that will appear when you are pointing your mouse to a blue space. Usually, selecting another unit and then going back to the one you want to move will solve the problem.
2) The "stuck-in-the-air" bug: when you start a turn with units that are currently flying, it's possible that some of them will be unable to move. The only known way to shrug it off is have the unit to go back to the ground (it doesn't cost a move and you can relaunch your unit afterward if you want).
3) Selection bug: Never use the mouse to select a unit, use the hotkeys instead. Clicking on your units is inconsistent and can provoke a glitch where you become unable to do any actions with your units.
4) Some of the gene mods are bugged:
-Never use more than one unit with the gene mod Hypersenses. If you have several of them, you will be unable to see the signal that is supposed to indicate an enemy presence. Invisible units will still be revealed in the proximity of your unit though.
-The Bastion gene mod that heals automatically its user will not work if you are not hosting the game and your unit is not in sight of an enemy.
And to finish, a few random tips:
-To gain some time, after commanding a unit to move somewhere, you can immediately select another unit and give them their own command while the other unit is still moving.
-Alien units with melee attacks are fun to play, but make your chances of winning really low. Also note that melee attacks don't work in diagonals.
-You can't shoot an invisible unit, but you can always throw a grenade at them (or any other kind of AoE attack). If they are using Mimetic Skin (Lurker), you may even blow their cover and reveal them.
-Certain things are visible to your opponent, even if your units are invisible or out of their line of sight: psi-links, buff indicators, smoke grenades.
-You can also hear psi-abilities and Mechs' movements by pointing your camera to where your opponent is, even if their units are in the dark.
-Remember that units who are both organic and mechanical can profit and suffer from all the characteristics of both types. The only exception are the Mechs, who are immune to fire and poison.
-Battle scanners occupy a tile and are detected by the Hypersenses gene mod as if they were an unit.