If a ship has zero flux and their shields off they get a +50 speed boost (+75 with a skill-perk, but the AI doesn't have that), this is probably how it caught up to you.
It should be noted that if you use a speed boost (zero flux or maneuvering jets) to go over your normal max speed but then lose the bonus you will not slow down unless you try to use your engines, in that sense the 'combat speed' of a vessel is not how fast it can go but the maximum speed it can accelerate to. Therefore, you can use the zero flux boost and then 'coast' towards your destination with your shields up and weapons firing, as long as you don't bump into something or have to change directions you will be going as fast as you would be if you were using the zero flux boost even though you aren't at zero flux.