It's incredibly frustrating. Any time you try to close off an interior space with fencing, the roofing will encroach. I don't think it always did this, but it certainly has been a problem for the last couple of months. I've personally taken to using the arches with fencing (found in the "windows" section of the build screen) in place of interior fencing. But it's definitely annoying.
There are a couple of things you could do, though, to get around it. Adjusting the eaves on various roof parts can help, but it doesn't look like that would solve your specific problems. Instead, you could break your roofing up into smaller pieces. Pull your existing roofing pieces away from the wall by one square, and use half-hipped roofing pieces to fill in the gap.
Hopefully they'll fix the issue with interior fencing. But until they do, the half-hipped roof is your best friend.
