I have a Squier Custom II Telecaster, and my bridge pickup is .. sunken a bit.. I've never noticed it before and I don't even know if its not supposed to be like that. The neck pickup is raised up a bit like normal, and its even height. But the bridge pickup is sunken down to the level of the pickguard on the 6th string side, but is normal height on the opposite side.

Is this a problem? Is it something I can easily remedy?
The screws on either side of the pickup raise and lower it. Clockwise raises, counterclockwise lowers. You can experiment with the height while you play to see how you like it. You can also raise one side higher than the other to increase bass/treble output.

Standard Fender specs are here:
Often time the factory, or any shop that fixes your guitar will adjust the pick-up height for you, it has to do with how the pickups get your sound (their like little microphones) . I'm not gonna say to not mess around with it, but these is a reason for the heights their supposed to set at, I would maybe look up the model of your tele to see the proper height, just so you know where to go back to if your unhappy with the resaults
That's why I linked to the Fender telecaster setup specs. It sounds like the pickups are not at the factory spec height, which is the whole reason for the question. If you can work a ruler and a screwdriver, you can adjust your pickups, there's not much to mess up.
The Custom II is the one with P-90s right? They have their height adjustment screws along the middle, in line with the pole pieces. if you want to raise the pickup a lot you need to actually take it out completely and stuff in some more padding underneath to keep it propped up. P-90s are very powerful though, they're not meant to be that close to the strings.