Bottles, even those from a homebrew shop, aren't infinitely reusable and will eventually crack as the structural integrity is stressed during usage. Think of it like hit points. A 12 ounce bottle has 12 hit points, for arguments sake. Every time you take a wing capper to it, you have the potential of inflicting damage. Maybe one point of damage at first, but as the bottle ages the damage becomes harder to absorb. So what was one HP damage three bottling sessions ago, is now 3 HP damage. Next, the act of opening bottle becomes so stressful it is inflicting damage, like a hord of flail snails. Eventually you lose your level six barbarian.
So what did we learn class?
1. Always have a cleric in your party.
2. Structural integrity basics.
3. Shit breaks.
4. Get a bench capper, it causes less stress on the bottle necks.