The cotyledons are fine the plant is doing the same thing with them as it is with those first leaves: sucking the energy/ stored energy out and getting ready to drop them since they wont help it anymore. Also like grorite said get some perlite or another drainage promoting material in your mix if/ when you transplant again. When you do that you could also bury the plant up to where the cotyledons are/ were to keep it from being so lanky. The buried stem will eventually turn into part of the root system.