In addition to @faugustom 's excellent suggestion regarding clipped external references, another possible item causing the gaps may be Walls on a layer that is frozen or turned off. Freezing a layer does not prevent Wall cleanup (nor does clipping an external reference). One common scenario is if you have existing-to-be-removed (demolition) Walls in the same file as existing-to-remain and new construction Walls. Freezing the demolition Wall layer will not stop them from trying to clean up with any other Walls that cross them. Use different Wall Cleanup Groups for existing-to-remain, existing-to-be-removed and new work Walls.
David Koch
AutoCAD Architecture and Revit User
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