There were indeed two different sleeping capsules used at the end of the film.
The first one, #06 (the number which the capsule is marked with), is the one in which Julia wakes up at the end. It's also the same capsule in which Jack finds her at the crash site, i.e. her own capsule from the Odyssey. Although, in the footage from when they approached the TET with the Odyssey she appears to be in capsule #04, but let's just overlook that production mistake.
The second capsule, #02, is the one Jack used to smuggle Beech and the bomb into the TET. We never get to see either Jack or anyone from the resistance retrieve it from the crash site, but we do get to see two people watch Jack take off after having saved Julia, so they could have easily grabbed one. We actually only saw two capsules being destroyed when the droids begun their killing spree, and considering the fact that there has to be at least two empty capsules there -- which the droids had no reason to destroy -- it's very possible that at least one survived the attack.