Probably just a miss. I thought the same thing was happening to me when certain DoTs were not being applied...but if you watch the numbers that appear when you toss a spell, it is the majority of the time just a missed spell. This will be more common the more difficult the content you are playing in, because these mobs require a higher Accuracy number for 100%.

(To iterate, lower-difficulty mobs require low Acc. numbers to have a 100% chance to hit them, but higher-difficulty mobs require higher Acc. numbers for a 100% chance to hit. Anything lower than 100% Accuracy on that specific mob can result in a miss. You can look up the different Accuracy caps for different content on the forums/web search.)

It could also be a lag spike, be these are few and far between (unless you have really bad internet). Most of the time the spell still applies with lag, albeit just late.