What do you have the Virtual AI Active Limiter set to? If below the default value of 144, move it closer to that number and see if it helps (this could account for several of your problems if using too low of a number).

To get an accurate view of units in/around an area, you really want to be debugging the Virtual AI module rather than marking units, which you can do anytime at mid-game under module options in the tablet.

I also prefer to use a slower speed for Virtual AI. I like 25% and 50% myself, depending on the kind of progression I want. Using these amounts, rather than the default, will slow the speed at which the virtual profiles move. The slower profiles move, the slower everything will progress (such as the opposing side taking back towns you've liberated).

I see this is an insurgency with an Asymmetric commander. Remember, civilians will be recruited from civilian recruitment centers (these need to be blown up) and turned into units for the insurgent side. It's very important to prioritize destroying these above all else if you want to stop the enemies growth. Make sure these (and any other OPCOM Installation, which you can also debug in the tablet) are destroyed before leaving an objective. And to hold an area, don't be shy. Bring in several groups to occupy an area you want to hold. One group won't cut it, especially if both sides deem the objective important.