All along I have made the mistake of selling my excess multiples directly from the nest. Sadly, I eventually realized I had lost XPs by doing that. I could have leveled up much faster if I hadn't made that mistake. Now I am sure to keep excess babies at level one (do not feed) and first sell a baby I have too many of. This makes room for the new dragon and I gain the XPs for placing in the habitat.
Another mistake I made initially was to keep no more that 2 of each kind and sell the rest even if I had room in the habitat. I finally realized I was losing earnings. Now I keep my habitats full regardless of how many multiples there are of one kind of Dragon. Eventually they are replaced by new other breeds.
I am posting this to help those that may be making the same mistake as I did. Especially those just beginning the game wanting to level up faster and earn more coins.
(honestly don't know why it took me so long to realize this )