The two key areas I'm aware of are the Condition Track and Skill Focus: Use the Force.
The issue with the Condition Track is that there are a handful of builds that can routinely make attacks that drop targets three or four steps down the track. Since this bypasses hit points, it allows them to take down far more powerful foes far more quickly than they should.
My suggested fix for this is to be very strict about allowing stacking of such effects. Basically, unless an effect states that it moves a target an additional step down the track, it doesn't stack, and don't allow multiple such effects to be applied at once. Even that may not solve the problem. (And others may well have better solutions to offer.)
Skill Focus: Use the Force is primarily a problem at low levels. Basically, it gives the Jedi +5 with all his skills, which far outstrips any 'balanced' opponent's defences.
My first attempt to fix this would probably be to remove both Force Training and Skill Focus from the list of bonus feats from any and all classes. This means that for the Jedi to get SF:UTF, he's had to sacrifice an FT feat (the other vastly useful feat for Force users).
If that didn't work, then my second attempt at a fix would be to put a prerequisite of level 9 on the Skill Focus: Use the Force feat.
Other than that, I think the only thing to really worry about is that SWSE is generally a much 'lighter' d20 game. As such, it hasn't had the same depth of playtesting (and errata) as either 3e or 4e. So if a player really wants to break it, they probably can. But your best bet for dealing with that is probably just to be open with, and cooperate with, your players - after all, they don't really benefit if they break your game either!