I don't think it is just the sky - in the photo you have posted, I'm pretty sure that the blotches are right throughout the picture, it's just that they are much more obvious on the sky.
I have to say that I think it is the negative or slide itself - especially as you say that it is not apparent with all pictures.
It may be that the neg / slide can be cleaned up, but this depends on the substrate - acetate (up to end of '70s) or polyester (from early 1980's).
If they are acetate, then that "bubbling" is a common sign of deterioration. Is there a "vinegar" smell?
I suggest a google around the subject of deteriorating negatives and cleaning negatives.
SD