We've all made this mistake. You go out and create a gorgeous panorama from a series of vertical/portrait photos. They're all shot perfectly with matching manual settings. The white balance is set, the iso, and on and on. Then you get back home and realize you forgot to take your circular polarizing filter off. This results in uneven photographs that don't match perfectly. When you blend them together it just doesn't work. It results in something like this:
It pains me to say this but there is no real easy fix for this. The only way to fix this issue is to avoid doing it in the first place or go reshoot. I've done this and it's painful. You can play around with photoshop and try to fix the issue but the best thing to do is avoid this in the first place.
One reason it's very difficult to fix is that the entire purpose of the filter is to change the light hitting your sensor. So as you move your camera across the scene for the panorama the filter is filtering out the light differently. In this way, the images will be vastly different as you pan across. The skies will appear darker in some or reflections may come and go.