Do you pin your animations to a controller sprite?
You can avoid many animation issues by using a controller sprite object. Simply make a sprite that has your "characters" collision bounds (ie scaled to character sprite size with appropriate collision bounds) and then set it to invisible. Give your character that is animating a pin behavior and simply pin it to the "controller" sprite when it's spawned. The controller spite would get all the stuff you would put on your player.. instance variables, movement behavior, physics.. etc. and the animations would just be pinned to its location and not actually interacting with anything.
In your example you could then pin other invisible sprites to the controller for sword collisions and such and match them to animations...