Using Flyby on a single target mob (eg: boss) is not an efficient use of energy, time or the global cooldown. It takes approximately 3 seconds to cast. For AOE mobs, sure, it's fantastic (and fun!) but not for a single target one.
To OP:
In future on Scrapper use Disappearing Act (especially since you would have chosen a talent which reduces the CD) and then stick in a Fletchette Round and Shoot First again - it's your highest damage so don't waste it!