Continuity mistake: When R2-D2 closes the door to the platform in the back of the monastery (before Asajj attacks Ahsoka), Asajj stabs both of her lightsabers through the door, a few inches apart from each other, and starts moving them downward. In the next shot, on the other side of the door, there is already a solid line (the top of the circle) cut into the door. There wasn't enough time for her to have stopped and connected the space between the two holes. (00:45:40)
Revealing mistake: When Anakin, Ahsoka, and the clones begin their ascent to the monastery on planet Teth, the ascension cable of one clone trooper (second from the front when the shot begins) is not animated correctly and a gap can be seen between the end of the cable and the clone's blaster. (00:35:35)
Answer: Canon in the Star Wars universe is a somewhat complex term as it has several levels ordered in a hierarchy of precedence. Facts stated at a certain level are considered as canon, unless contradicted by something at a higher level of canonicity. The uppermost level of canonicity are the six live-action films. Lucas has stated that the television episodes (which include the Clone Wars movie, which can be considered as the first episodes of the TV series) are to be considered as the next level down in canonicity, so below the films, but above any other releases (books, comics and so forth). So, basically, yes, they're to be considered canon, except in any case where they contradict something established in the live-action films.
Tailkinker ★