There is a difference between the two, but you'd definitely have to call your pharmacy (or better yet, go back to the pharmacy) and ask which one they gave you. If your doctor prescribed extended release, they have to give you extended release and they should replace your prescription if they've given you the wrong version of the medication.

I am prescribed the extended release version of Wellbutrin and have taken the regular version before and have only noticed minor differences, but my pdoc definitely prefers that I take the extended release and really, I prefer it as well.