Your patrol forces may be too small. If you automate a fleet, the computer will decide to send it against targets that have less than some fraction of the fleet's (or ship's) strength (maybe just firepower; I don't recall at the moment). This ratio can be set in the game options menu during play.
Another possibility is that your fleets decide to go attack the target, and run low on fuel halfway there and therefore turn around and refuel, and then get assigned to a. another job, or b. the same job, for which they still don't have enough fuel. The only reliable solution to this issue is to ensure a better supply of fuel to the area of operations (Resupply Ships, starbases with gas extractors on Caslon/Hydrogen sources as appropriate, gas mining stations, etc), or design your ships with greater operational ranges.
A further possibility is that your patrol forces may have more important targets available to them, however the computer defines 'important'.
It may also help you to have Long-Range Scanner coverage of most or all of your empire; I think the computer tends to prioritize targets for which there exists a recent sensor contact, and even if it doesn't scanner coverage will allow you to see stations on the main map without selecting the system or zooming all the way in to the system view.