That’s due to modeling method. Logically the roof planes should work as shown, You just got some inaccuracy into the model somehow, and You either live with is or start over. If you wish to do a lot more with the model, I’d start over.
You could use groups to keep parts separate until you ready to combine the different elements without messing up the planes.
Different plate heights do require finding a special approach. Maybe there are some other ideas out there. I admit I don’t have a specific method for this situation. I would probably just “model at it" using inferences once I established the pitch.
For regular roofs, your hips are all the same angle so you can use one hip to copy from or use as a inference for another.