According to Wikipedia:
The pronunciation of the digits 3, 4, 5, and 9 differs from standard English – being pronounced tree, fower, fife, and niner. The digit 3 is specified as tree so that it is not pronounced sri; the long pronunciation of 4 (still found in some English dialects) keeps it somewhat distinct from for; 5 is pronounced with a second "f" because the normal pronunciation with a "v" is easily confused with "fire" (a command to shoot); and 9 has an extra syllable to keep it distinct from German nein 'no'.
The phonetic alphabet is not a random selection of words. It was created very carefully taking dialects into account, so as not to confuse any of the letter with possible mispronunciations. Although they are "English" words, the choices were made with the world in mind.
As mentioned on the same article:
The final choice of code words for the letters of the alphabet and for the digits was made after hundreds of thousands of comprehension tests involving 31 nationalities.