Two issues so far:
One, abilities no longer indicated if they needed a specific weapon class (on a Jedi Knight story with Shadow) - taking an upgrade training saber can lock you out of breaching shadows, hover over there says wrong weapon but not which to use.
Second - When I levelled up to 4 on Shadow it rearranged, while in combat, my main taskbar (as opposed to adding new abilities or powers at the end) - project went into the second slot as far as I can tell and pushed the current second slot to the fourth.