Clone Wars - Canon?

With the fact that there is now around 40/50 Episodes of TCW that have been shown, how long is it going to take for it to mess up continuity? Because there is some battle or something every week, and the time it takes to travel between the planets might be a while, so it will end up being more than you can fit into 3 Years of war. I have seen 5 Episodes of TCW, and all of them have been Anakin, Obi-wan and Ashoka, even though Ashoka was only in the first two that I saw, and the last 3 have been recordings on Sky. Unless they do episodes based on the less known jedi/clones (Bly, Bree, etc) and at the same time as previous episodes, it will end up making no sense. Also, in a episode a few weeks ago, there was this ship that could turn invisible. How come this technology isn't used by the Imperials a few years after TCW? TCW has already started inventing stuff they didn't have in the Original Trilogy, which also makes no sense.

This is the thread you're looking for:
Clone Wars Continuity & Canon Thread