One quick diagnostic would be to group everything that should be flat and then scale it vertically by a really large number. That would make the offending nonplanar geometry easier to identify. Just remember what you scaled it at so you can scale it back down.
Otherwise if your geometries are more complicated than flat geometries, I’ll just start drawing triangles between what I think should be coplanar edges. Once the offending end is identified, you can move it and infer the plane it should be on.
Third thing is to turn on hidden geometries. Sometimes hidden folds just happen. In this gif, I am tapping the “up” arrow key to lock the corner move in the blue direction when I reference the slope from the upper right portion of the roof.
Just thought of another diagnostic. If your model is orthogonal, you can set your edges to be colored by axis from the Styles dialog window. In this example, the offending line should be green.