Sometimes SRB2doombuilder has a hard time defining sector walls, and glitches tend to happen, I usually check sector mode to make sure my sectors are functioning properly before I continue, I'll point that out to you right now. And in my experience, it happens a lot when you paste multiple sectors at once, or split sectors in odd formations. One thing you can try is go around the map and complete the sectors yourself, but I can't guarantee how it will work. I know I'm not much of a help, I haven't used SRB2Doombuilder a lot, but I'm trying.