Geth Hunters make heavy use of cloaks and are almost impossible to detect, unless you observe keenly or shoot at them. Are there any ways to highlight them and find out where they are?
All cloaked enemies "shimmer" slightly, which can help you find them if you know approximately where they're moving.
If you just don't have a clue, open up with an automatic weapon and walk your fire across the general area. Area of effect attacks are pretty good at exposing them as well. Weapons like grenades or mines, or powers like Singularity can help.
In general, once you've done damage, their cloak will fail temporarily, giving you an opportunity to target them and do serious damage.
Another tactic which kind of works "by default" is to just wait for them to flank you - if you know they're coming, stay in cover and wait for them, and then target them with short range, high power attacks when they decloak and start to attack. It's risky, but if you're low on ammo/grenades and can't employ these other strategies, you might not have many other options.
Equiping the Javelin sniper rifle can help, as it highlights cloaked enemies in a purple outline (similar to how the Sniper Rifle Enhanced Scope upgrade allows you to see enemies through smoke).
Additionally, since Hunters will temporarily decloak after taking damage, spamming powers with a wide impact radius or homing capabilities (i.e. Incinerate) might also prove to be an effective way to weed them out before they're on top of you.
That said, I found that they usually weren't too hard to detect if you look down range through a scope since you can typically see their distortions as they move across your field of view. After that, it just takes at most a few shots to expose them, and then some directed fire to lay them down.
Shimmers are the best method of detecting Hunters. If one decloaks, it's in shotgun range so move. If they decloak it will take time for their cloak to reactivate. AoE powers are useful if they're in close proximity. If a cloaked hunter takes a hit, it will provide a target lock for homing powers such as biotics, tech, and impact (carnage, and concussion shot) powers. The window for this is small so make sure you hit it the second you can see the health bar.
Also if a Geth Hunter doesn't have shields, IT CAN'T CLOAK. So if you see a Hunter without shields, DO NOT let it regenerate those shields even by 1% or it will be able to cloak again.