Good job of not overreacting before you had the facts. Many owners would take the manager at face value and potentially end up losing a good tenant and creating liability.
Clearly the story makes no sense. It would appear that the manager is making things up. When you lose faith in the manager being 100% honest, you should change managers. Otherwise, can you trust the other things they tell you going forward?
Are they falling behind on any other duties? is this a single event or a growing trend?