Look, the basic problem is most likely the limited color resolution you end up with if you're going to press down the highlights a lot. The highlights on negatives are tricky to begin with especially if you scan them. Firstly, extreme highlights such as the well-lit edges of clouds tend to cross over a little anyway, especially on a film like Ektar. Secondly, those high densities in the negative are a little harder on the scanner, reducing the signal quality in those regions.
Then in the digital domain, things don't get all that much better either if you take a tiny bit of the curve (i.e. the highlight regions) and then start stretching it all out. Contrast goes up, but of course saturation also goes up, since an expansion of contrast means you're also amplifying differences between the color channels. This is your major issue currently and all you can do is selectively reduce saturation in only the affected areas with adjustment layers.
TL;DR time to learn more about adjustment layers and masking of adjustment layers.