So there are two major bugs with the supply system at the moment. They are:
1. Stationing a ship in a port and placing a land unit on the same province prevents any local supply hub from providing supplies to the land units. The land units can only draw supplies from the very limited state supply pool. This makes guarding ports that are actually being used very difficult and makes naval invasions impossible in most of the pacific, where single province islands with ports, like Guam and Iwo Jima, are the norm. Without the ability to naval invade the US, UK, and Japan can't have a pacific campaign. Thus these majors are unplayable in a historical game. This issue also affects Malta, which really messes up the ability of the UK to fight effectively in the Mediterranean.
2. Supply hubs cannot provide their full supply amount to a single province, even if their supply area only has a single province. This prevents you from concentrating your forces for an attack or effectively garrisoning small areas. Once again, most of the pacific and Malta. Guam is a good example here. Build a max port in Guam and LA, max railways between LA and Washington DC, a supply hub in Guam, fully motorize the Guam supply hub, build and max infrastructure in Guam and the entire continental US. Then check the supply map. Despite having a supply link to the capital of 35, Guam can only support 7.44 supply worth of units, and only if you don't put a ship in the port. (If you put a ship there, it can only support 1.8, not even enough for a garrison, even if you use logistics companies.) This is probably the bigger of the two bugs as it prevents anyone from making effective naval invasions since there is no way to stack say, 20 supply worth of units in most of the world's ports for a naval invasion.
Both of these issues have been mentioned in other threads and acknowledged by devs. Hopefully they will be fixed soon.