can you put a screenshot of what you're seeing up? I'm seeing the filled heavy rough removing trees properly.
What theme were you on when this happened?
It happened to me on the Swiss theme, first hole I placed. I wanted to push the tree line back in places, so I outlined the entire hole with a HR spline path, closed the path, smoothed the path, then auto-filled it. The HR drew in correctly without holes, but many (not all) of the large autogen pine trees were still there, right in the middle of all the new HR. It seems to be an issue just with certain trees. Give me a bit to grab you a couple screens, I'll have to go in and delete the remove autogen tree brushes to get it to show up again.
This is on PS4 btw, if that makes a difference.