After hitting level 3 of my city, the trucks started to disappear. The trucks would all finish to their destination and then NOT reappear. Once all the trucks made it to their destinations, the city starts downgrading the habitats due to the lack of movement of the resources. This happens about every 10-15 minutes now. To solve it I have been saving and reloading my city. After reloading the city all the trucks start coming out of the buildings again.
I am having this issue as well now.