While trying to buy a box of energy cells (bulk) from Chet in the starter town I noticed something quite nasty. He was taking my caps and not giving me squat! I only noticed because my inventory was empty at the time. Otherwise I wouldn't have even known it until I tried to load my weapon.
Here is the video: http://www.youtube.com/watch?v=yOn0-5pHTdI

I got something similar to that as well when buying .38 Special rounds, I could find I could buy one box but not another as chet kept taking my caps!

Found a workaround. It's clunky and svcks but it works. I had to save and exit the game completely (all the way to the desktop) and then reload. After that it let me buy the ammo normally. Just reloading or leaving the area and coming back didn't work.