Not all trunks, branches are created equal; both branches look like Meyer; and it is not uncommon for a tree producer to put more than one bud to speed up growth and development of the tree. Sometimes one bud just "takes" better than the other; over a longer period of time, you should see them more equal. BTW, for plants in the ground, the roots tend to follow the water and fertilizer; so if you put the fertilizer and water on one side, the roots will grow there, followed by the limbs. In pots this is less likely to occur; but perhaps you put more fertilizer on one side; or maybe one side of the potting soil is packed more tightly, or something else is inhibiting root growth. Could be a simple as when you planted it, it had more roots on one side; or you damaged some roots on one side. The rule is, first the roots grow; and then the leaves/limbs follow.

Thanks! So I guess that I shouldn't be too concerned about the "Y", and it will just grow up to have two main branches huh?

It'll proly grow up to have half a dozen or more main branches. Not to worry; give it TLC and have a little patience; your Meyer will reward you with the best lemon in the world... I have 7,000 trees, so I'm more than a big fan.