Covert scanners will detect you since:
a. got too close
b. covert (hence covert scanner detection device)
Negative faction points really don't matter as much as the fact that the covert scanner is up and running. The max that you can have in any faction is -5000. Just make note of where those scanners are. /shrug hope that helps. I always assume that there will be covert scanners up in any player made city/outpost and I take careful steps to have an escape route, until I get to know the town a bit better. Makes the game a bit more exciting though! Hope that helps you a bit.
"Truth is always paradoxical"
-Henry David Thoreau-