I had the same problem with mine in the past. There are two things that go along with this problem that I found.

So, the first thing...
See this picture: http://forum-s3.pinside.com/201311/1282092/160206.jpg
When the ball kicks out there are two metal "flaps" that direct the ball to the correct location as it's leaving the trough. When these got bent, the ball would not exit correctly and then bounce back into the trough.
You just have to bend them back to the correct position.

The second thing is "why is this happening?"...
On mine, it turns out that my shooter wasn't correctly centered on the ball and sometimes it would end up shooting the ball into the metal "flap" during multiball when things were going fast and crazy.
Here's my thread where I fixed that problem: http://pinside.com/pinball/forum/topic/hs2-plunger-alignment
Before I aligned the plunger as shown in the thread, I was getting this problem repeatedly every so often. Now, that I've done the fix, it hasn't occurred again.

Hope this fixed your problem. I know how annoying it can be when the ball won't leave the trough.