The hub is accessed through doors, there's no way of getting there by using the warp gates alone or from a random location. Usually you need to navigate to the nearest map node which is connected to the central hub, then search for the door that leads there.
Locations with many doors can be confusing, so pay attention to the map, especially since it also marks all of the warp gates you encounter.
The regular warp gates - the large four-sided ones - can transport you to another hub (where there's a tree growing on top of the gate - that gate is the first one you see in the game). If you manage to get there, just go to the bottom of the location and look for the door to the central hub.
The smaller warp gates, which often appear in "secret" locations after you solve a puzzle, transport you to the nearest regular warp gate.
There are also shortcuts in many places (those small doors with two squares), one of which could potentially take you to the hub with the doors, but I have yet to fully understand how those work. :-/ Apparently, you can only go through them if you've already been on the other side.
I tend to get lost very easily in this game, spending lots of time just searching for the correct door. It's not bad near the beginning, when most doors are closed/locked, so you can tell whether or not you've entered them before. But later it becomes important to memorize which door leads to where, since the game is designed with a lot of backtracking in mind (e.g. when you learn numbers or alphabet and have to return to places which use them as puzzle elements). But then, you don't do much besides exploring the locations anyway...
