I had a fleet of ships with short range beam/cannon weapons. I set them to the sentry fleet command and spawned a pirate Isanth ship with cannon/cannon weapons about 2km away. It kept shooting at them and they never fought back, never moved. I tried switching them to the defend sector fleet command for their current sector. They still did nothing. I destroyed the pirate ships and spawned it within 1km of them, and they started fighting.
It would seem that fleet ships ignore everything outside their weapons range. Even if it is Killing them.