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My guess is that you have a single object (airplane?) moving across the scene and that you photographed it multiple times, so you have a lot of overlap.
My suggestion would be to let Hugin align the images and let nona warp them. Select only a few to generate / blend the background, then load that background plus the warped individual images into Gimp or Photoshop and overlay the multiple shots of the moving object, masking the alpha channel. A feather in the alpha channel should be enough "blending".
Other than that (and than recommending trying with Enblend 3.x and alpha masks as well) I don't know of anything that could be done with the report other than say, sorry, won't fix...