Here is my theory.
People started to make fun of Edward's size the moment Alphonse equaled and surpassed Edward in height.
Think about it. Alphonse and Edward are kids growing and then one day, Alphonse equals Edward in height. Everybody goes, ¨Woah!! Al, you really grew. LOL, Edward, your little brother is the same size as you. LOL, that's funny.¨
Then the big day came. Alphonse is now taller than Edward. Everybody goes, ¨Wow!!! Alphonse, you are bigger than Edward now! You look you are the big brother instead of Edward. LOL, Edward, you are so little! Your little brother is bigger than you. LOL, You are such a pipsqueek, Edward!¨
People started making fun of Edward's size when Alphonse passed Edward.