So as I understand this, you've now got two plants growing in the same area/pot... correct? Sadly, you're going to eventually get it down to only one plant (the largest) but I would NOT try to lift the other one out and transplant it - you're more likely to screw up both of them to the point where neither one is viable. If the cotyledon is showing on the smaller, newer growth, you can take some scissors or a very sharp knife and CAREFULLY snip the stem just under the cotyledon off thus killing off that plant/seed... you can also wait a week or two when the stems have grown more and there's less chance of cutting something you don't want to cut (like the stem of the larger plant). But you're going to HAVE to kill off that smaller growth - two plants in the same pot are a recipe for disaster.
Good luck...