VXLAN Flood List Routes - Missing Routes are seeing when the Leaf's Generic System -facing interface (where CT is assigned) is down. 

This is Junos (Leaf device) behavior. When the GS-facing interface is down, the leaf device does not send routes to other leaf devices, causing VXLAN Flood List Routes anomalies.

Please try to have the interfaces up and check if the leaf devices start sending routes to other leaf devices.