As you complete the missions in the game, you will undoubtedly use a lot of the same tactics for them, whether they be stealth or run-'n-gunning. The only problem in doing such a thing is that enemies will adapt to your tactics by doing certain things. For example, if you keep shooting enemies in the head, whether they are lethal shots or non-lethal, they will eventually start wearing helmets.
You can check whether the enemy have prepared such methods by looking on your map. On the right hand side, there are icons that will be highlighted, meaning the enemy have tried to counter your tactics with their own. Each of these has different levels, causing the enemies to add or do something different, with the icons having a white background for the first level, then pink and red for the second and third.
There's nothing you can really do to combat this, but the Dispatch Missions that unlock later in the game will add something to temporarily provide a solution. These Dispatch Missions are quite challenging and will require you to have high-ranked personnel in the Combat Unit to send out on them. Note that some missions in the game will always have a certain type of enemy, so the dynamic difficulty doesn't apply to them.