PROBLEM:
You join 2 separate walls in plan by dragging one to meet the other.
One of the walls had a top or bottom offset, or was joined top or bottom.
After joining them both walls have the same top or bottom offset.
CAUSE:
When joining wall that are of the same type Revit 'helpfully' turns the two walls in to one wall, so the joined wall takes on all the properties of the other wall.
SOLUTION:
Join the walls in elevation instead of plan.