Could just be latency/delay between your timer and the timer server side. :01 of buffer is way to tight to guarantee a success. Also the timer you see is client based and not server based, so players could end up having different timers (noticed that during ifrit battle, when someone called time when pillars pops, there was a good 5 seconds (at least) difference with my own timer)
Same issue existed in XI as well, I remember getting a Dynamis time extension exactly right the time was over, in the logs it would say : "Time has been extended by 30 minutes" and right after "You'll be removed from the area in X seconds".