Having brushes inside a skybox brush causes them to have shadows most of the time because despite the skybox brush emiting the light, it doesn't let any light through.
I don't know why Source does weird things to brushes intersecting skybox brushes, or how to stop it but....
Thoughts:
It's entirely possible that a displacement face might not suffer the same issue, and since sheet metal on a roof is often made from displacements, that might be a good solution here.
It could be caused by lower than max compile settings. If there are fewer bounces, or rays fired that could easily cause something screwy. Try doing a compile with -final if you haven't already
That's a rooftop, it won't be seen much and by the looks of how they should be lit and shadowed, the faces should be fairly even. You could mask the issue by dropping the lightmap size to 64, or even down to 256+ to smooth out the entire face to just one or two luxels
And for the nearer roof, these both look like smoothing errors so:
Use hammer's smoothing groups to manually separate these faces
Change -smooth in vrad to a lower value, the default is 45 and any two faces with an adjoining angle below that will be automatically smoothed
Change the lightmap scale on one of the faces to be different from the other, this will prevent them from being smoothed
Make the angle steeper or hide the error with another brush
For the near, thin, roof it looks like it's smoothing with the face touching the wall as well as the other side of the roof, simply nodraw that face
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