If you can move the negative so that the portion to which you are referring is placed directly below (or as close as possible to) the optical axis of the enlarging lens, with the aperture set to two or three stops smaller than wide-open, then do a series of test strips of this area - honing in on exposure and contrast...this should tell you something.
When you'd mentioned the fog rolling in...my first thought was light scattering by water droplets in the air. My second thought was that perhaps the branches were moving ever so slightly during the camera exposure. More remote possibility that your use of a diffused (enlarger) light source could be placing the very thin branch areas beyond the exposure threshold of the paper at your settings.
A question: what enlarger lens are you using? Do you know that it is in good condition...collimation-wise? A hunch: Despite Beseler's decision to go with a tilting lens stage to help with "after the fact" corrections of converging verticals, I've never trusted these stages and wish that that Beseler had either made such a stage optional or had done away with it entirely.
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