Hi Caylian...
There are no config options for this. Unfortunately this happens frequently on flattened harnesses. I got in the habit of making a "break symbol" that mimicked the squiggly break lines you'd typically see in a broken view. Then, I added that symbol to the appropriate place in my broken view and related the symbol to the view. If you don't relate the symbol to the view, if you move it (the view), the break symbol won't move along with it.
I hope this makes sense. In summary- you're not seeing an error, just a limitation to the way the flattened harness works. The break lines don't show the way you'd expect. Manually adding in those break lines as sketches or a symbol is your only way around this problem.
Thanks!
-Brian