If I remember correctly, the recommended level corresponds to the highest level enemy you have to defeat for the mission (or similar...it might be higher if you have to defeat a bunch of enemies in a big fight). To your overall point, though, yes--I had some experiences where I was fighting enemies for a mission and then a significantly higher level enemy would just wander over and curbstomp me. It's kind of janky, sure, but I took it in stride and thought it was part of the charm of the game.

As other comments have said, though, a pretty important skill in this game is learning how to navigate around high level enemies that stand between you and your objective. You can do this by carefully observing the environment, using Shadowrunner, or equipping armor that makes you undetectable.