Yesterday I tried to make a new character using the fairy race. Everything worked, but when I was looking at my spell list, I noticed that I have Faerie Fire listed twice. Upon investigation, I realized that the second Faerie Fire replaced the enlarge reduce spell that I should have as a fairy. I have played a few fairies in the past, so I know that this is a newer development. Please look into this. 

Please post a link to your character. I think the duplication is because one entry is the 1/long rest entry and one is the castable entry. At least that’s the way it displays on my fairy character, for both faerie fire and reduce/enlarge. 

As ArwensDaughter explained, one instance of the spell says “cast” on the button, the other one says “use.” That first one is for regular casting using spell slots, the second one is for the 1ce/LR casting they get for free. As for enlarge/reduce, you don’t get that until you hit 5th level.

I've also had this issue, made a fairy light cleric, level 3, have three lots of faerie fire, under my 1st level spells?? 

Yes, one instance of that spell says “Use” and is the once/day free casting you get as a Fairy, one instance says “Cast” and represents the Fairy’s ability to also spend spell slots to cast the spell, and another instance says “cast” and is the “always prepared” spell you get from your subclass.