How to make a fillet to flow along a curve
I've tested your problem using two designs but it didn't show any anomalies like yours. Take a look at them. I may think that's a problem with the geometry in the fillet area; may be the side faces are not tangent. I couldn't decide with the limited data you've provided.
Looks like Gilhan got it working.
When making the fillet, look in the feature tree for something like "Fillet Options". There is an option which toggles between keeping model faces, and some other setting. I hardy ever use it, but try turning the option on/off and see if you get a different result.