In the PlanAhead 14.5 and later tool versions, the Undo of a drag-and-drop of a port in the Package View results in a duplicate ports constraint.
If you drag-and-drop a port in the Package View, then use the Undo option to remove the constraint, the previous location is restored but the new location is not properly deleted.
This issue is with the PlanAhead tool only. The Undo functionality has been rewritten in the Vivado tool so that this issue does not occur.
The Undo of drag-and-drop of a port placement procedure should be avoided in PlanAhead 14.5 and later tool versions.
To correct the dual placement constraint, select and delete the constraint from the location you do not want it to appear.