Yes, this has been happening for me when try to create an open 2 story stairwell by deleting some floor tiles and fencing off the open area. I have found no really easy way around it. But there are some things you can do to get rid of all or most of it depending on the build and what you are trying to do. There is something going on with fences and roofs here. Octagonal roofs do the same thing too.
The biggest thing you can do is look at how you are using the roofs on the lower level. See if you can find a way to get the look you want by using separate roof sections rather than using a full roof or like in your pics, a half roof so you can get roofs on 2 sides. If you can, keep all the roof sections out of the upper floor spaces. From what I can see in your pics, you could use 2 half hip roofs, one on each side or a half hip on the front and a gable on the side depending on the look you want.
Working with roofs to get the desired look can get really tricky at times so you just have to keep trying different combinations until you can find one that you like or at least you can live with.
Hope this helps.
