This isn't tied into Mental Alacrity. It's just a server-side lag issue, usually referred to as input lag. You punch a skill, you lose a GCD, but the skill doesn't execute. Usually this is coupled with the visual effects of the skill in question. Say I was trying to use Telekinetic Wave: my Sage would throw her hands up in the air, as she would when casting it, would hold this position for about 2 seconds, then return to normal.
Seems like this would be a problem for Mental Alacrity because you're relying on firing off more casts: if more of them get lagged in the way you describe, it reduces the effectiveness of MA.