This is a hidden strength of Gunbreaker, not a weakness or problem. It means that, while No Mercy is on a strict cooldown, you have some latitude to delay Gnashing Fang, Double Down, and Sonic Break by some amount if necessary/forced and they will gradually re-align themselves as the fight goes on.

Obviously that won't come up during an optimized run where your GCDs are known beforehand, usually won't have much effect, if any, in a run where everything goes smoothly and according to plan, et cetera, but part of the reason Gunbreaker tends to have a more smooth play experience than other tanks is that the effect of Skill Speed on its GCD Cooldowns causes its rotation to self-repair a lot of minor mistakes in a way that you don't get on Paladin or Dark Knight.