Also very common as a nickname in Brazilian Portuguese. And not only for Rafael (M), but also Rafaela (F). Rafa is common + unisex. I noticed it's probably this common only here in Brazil, in Portugal "Rafe" is more used.
A Spanish masculine name almost always ends in "o", "e", or a consonant, but this name ends in "a". But this makes sense, since the original "long form" is "Rafael" which ends in a consonant.