Since the last patch (one of the bug-fix patches I believe) Mantras have started counting down their cooldown timer immediately after charging rather than after the final charge has been used.
Effectively, a mesmer can can now charge their mantras in advance of a fight, use all the charges, then recharge the mantra immediately. Before the patch, the cooldown timer would begin after the last charge had been used.
I assume this is a bug rather since it is different than before the patch.