Cafe Appearing in the middle of the biodome: This is a conflict with an item in the biodome with the California map, disabling it solves this problem.

Missing structures, objects not appearing in map: This is caused by not having the required workshop items installed or enabled, make sure to take a look at the workshop page to make sure you have everything installed and enabled in-game.

Item ID Conflicts/Items Not Spawning: It is more than likely that you have a workshop item that conflicts with the item ids of items that are supposed to spawn in the map, find what item is or if something is simply missing, try disabling your other workshop items.

If anyone else has other issues they've encountered, make sure to share in this discussion.