Ordinarily, the distinction you will have is in the pronunciation of "w" sounds -- some pronounce it as "v" and some as "w." So the sixth letter of the Hebrew alphabet is pronounced "waw" by some and "vav" by others. Along as you understand the difference, it's no big deal. I had a Hebrew prof who would sometimes slip up and start writing the letters in Hebrew cursive. Believe me, that's next to impossible to read, and we'd always have to stop him.
Other languages do the same thing. In Greek, I learned to pronounce letters ending in iota with a short "i" sound (so e-ota instead i-ota). Chi was pronounced as "key," pi was pronounced "pe", etc.
But even the English language does this. Lots of people pronounce the last letter of the alphabet differently. Canadians sometimes say "zed." I remember reading an old article by B.B Warfield where he used the term "izard" to refer to the letter "z."
