If you see some of your flights in red on the map that means you have up to 15 flights of this route in your statistics. If you're getting closer to have the same flight route 15 times then you will see this flight will change from blue to dark red on the map and when it's going to be the 15th flight it will change it to bright red.
Below you find out some screenshots on how should it look like on the map:
If you made closer to 15 flights with the same route, then the blue color will change to red on the map
When you're getting closer to your 15 flight with the same route, this flight will become dark red on the map. When it will be your 15th flight it will turn to bright red.