Thanks for contacting the World Warfare support team.
Our developers have been made aware of an issue with resources and armament not showing up with transport vehicles arriving at destination cities after returning with troops.
We do encourage that you check your battle messages (click the Message icon) and then check if your transport has been attacked. There is a known issue where the message logs will not indicate any notification that your transport was damaged. You should now be receiving a "damaged supply warning" notification to combat this every 10 minutes!
As a side note, you will lose resources or armaments while inside the transport according to the HP it lost. In other words, the transport plane is damaged, so are the resources and is based on how much the HP the plane has left. If your transport hasn't been attacked, then we need to know the departure/destination city number, coordinates and resources you transported.
We apologize for any inconvenience this has caused you.