There are so many different frequencies emanating from so many different devices, organic life and even the Earth itself that it is difficult to detect all these waves. In the battlespace we often are able to detect enemy frequencies and often pinpoint their origin and thus able to target that electromagnetic signature. Unfortunately our systems often do the same.
One tactic used to stop the enemy from communicating is to use an electromagnetic burst to take out all electronic devices. Yet in doing so you lose your ability to see the enemy