Go back to the design screen and take a further look. Change the resolution of the scanner to "1".
In the field you will see that the detection range of your scanner is 10m kilometer for a 50 ton object (1HS) and the range will reduce further the smaller the object you want to detect. A size 12 missile would be detected at 3.6m kilometer, a size 8 at 1.6m kilometer and a missile of size 1-6 at 1.1m kilometer.
So you are not fooled.
If you want to detect missiles further you either need to build a dedicated sensor ship for missile detection or use small escort ships around your TG to extend the range of the missile detection possibility. I use the latter because I find it more fun. I build small escort frigates with a small resolution 1 sensor and some size 1 launchers and AMM. Small enough (around 3500 tones) so they are not detected and fired upon by enemy missile ships.
In addition to this my capital ships (some of them) might house a small hangar of say 500 ton and keep an early warning craft that has a size 6 resolution 1 scanner. Very useful to get additional missile tracking bonus for your point defense guns.
In my current game my CIWS and half sized Gauss cannons in turrets normally has a around 60-90% chance to fire on incoming missiles. In my last engagement the CIWS system had almost a 100% chance to hit and knocked down far more missiles than my rather poor AMM.
In my current game I have a total missile tracking bonus of 60% so and my Gauss turrets and CIWS has a tracking speed of 16000. With extending the missile detection area I can usually get a very high to hit rate on missile at up to 35-40000km/s.