You may encounter this warning when you add or move a room separation line that overlaps an existing separation line.
Warning: Highlighted room separation lines overlap. One of them may be ignored when Revit finds room boundaries. Delete one of the lines.
Solution: Select one of the room separation lines, and delete it, move it, or change its length, so that it no longer overlaps the other line.
In some cases it may be difficult to identify room separation lines. You may consider applying a visibility and graphics override to the room separation lines. <Room Separation> is a subcategory of Lines on the Model Categories tab in the Visibility/Graphics Overrides Dialog.