Sorry, the video is kind of fast.
Throughout the video you can see a white / very light blue colored feathered edge around all the tree branches... that is a form of light bloom. When the hoaxers tried to chroma key out the background (the solid blue sky), they didn't do a good job of keying out the light bloomed feathered edges of the branches, and that caused the light bloomed areas of the sky to appear on top of the UFO.
Some of the small gaps between the tree branches were completely filled with light bloom, and that caused the small gaps to be a different shade of blue than the rest of the sky. When they chroma keyed out the darker blue sky, they didn't key out the small light blue gaps, and those small gaps of sky (which should have been filled in by the dark UFO when it passed behind them) were displayed on top of the UFO.
Throughout the video there are many small gaps between the branches which you should have seen the UFO between when it passes behind them, but instead they just show the sky. Those areas didn't get keyed out.