Broken-Line stitching errors
There may be no way to fix these in Hugin itself, as it's very probable you have a parallax issue when shooting. If you do not rotate the camera/lens combination precisely around the no-parallax point (NPP), particularly in smaller enclosed spaces, then you are creating issues that no stitcher can fix with any amount of warping, because objects will have moved, relative to each other, between shots.
Make sure you have your gear calibrated correctly, or at least that you are using some form of mechanical aid to rotate correctly around the no-parallax point (NPP). A plumbline is a good, low-cost way to begin. A special two-arm panorama head is probably the simplest way to go. Make sure you know where the NPP is in the specific lens you're using. If it's a zoom lens, make sure you know where the NPPs are for each given focal length.
See:
You may want to get Hugin to create layered output so you can use mask and layers in Photoshop or the Gimp to try and adjust where the breaks meet or to hide them if there's enough overlap from better-fitting member images. But this can be incredibly tedious, time-consuming, and futile in the end.
Fine-tuning Control Points
If you are certain that it's not parallax error, but that Nona/autopano-sift-c has merely mismatched control points, there is one simple thing that you can do, which is to delete the worst control point pairs.
Each pair of control points, when the final warping is done, is "scored" with a measurement of how far apart the two points are in the resulting image. In the Control Point window, you can sort by that distance, and delete any with very high ('out of whack') scores, and then rerun positioning optimization to see if everything shifts into place better.
In the Photos tab, at the bottom of the window, are the two Optimise options. The Geometric settings are the ones that control how the images are warped and positioned relative to each other with the control points.
However, Hugin does not yet have a feature similar to PTGui's "Viewpoint Correction", which can adjust for a shifted camera position. The "View" corrections offered here are for field-of-view (i.e., if you took member images with different lenses).
Clicking on the calculate button for the Geometric settings will rerun the optimizer. Checking how your control points score, or looking at the preview can help you see if there's been an improvement.
Ghosts and Clones
Ghosts and Clones are basically because something moved between the member images. In this case, overlap determines whether or not you have enough "clean plate" to use blend masks to erase the ghost/clone.
The Masks tab is where you can draw polygons around areas to exclude or include in the final panorama. It's a little cumbersome, but should work.
The main reasons I ended up paying for a PTGui license was for the better masking feature and viewpoint correction. :)
