When I try to buy bulk energy cells, they usually have 2 boxes. I buy the two, and I get 100 bulk energy cells, the amount for 1 box.

After noticing this, I try to buy them separately, as buy 1, pay for it, buy the other, then pay for it. But when I buy 1 box, the other disappears.

Is anyone else having this glitch or is it just me?

Well my suggestion would be to buy them one at a time but leave the vendor inbetween.

I tried that, but it didn't work. The second box disappears right after you but the first one.

Same thing happens with the Combat Armors at the Hoover Dam vendor. They only have one item, but more are shown in the inventory, so you can only buy one of them and the other disappears.

I think the other is there, but it is somehow hiding underneath the item. Try dropping the one you have and see if it is there. It won't fix it, but when you run out the other should appear.