It's not uncommon for Google (or other hardware manufacturers) to make subtle changes to devices post-release to fix problems that went unnoticed before the device hit hundreds of thousands users. That's exactly what happened with the Nexus 4, and it looks like the Nexus 5 is getting some hardware modifications of its own, as well.
As pointed out by XDA user shinral, the updated model has more rigid power and volume buttons, the SIM tray fits flush with the body of the phone, and probably the most visually noticeable difference, the speaker grill holes are now larger. Take a look.
Top: new; Bottom: old
These changes are, of course, an effort to fix some of the primary complaints we've heard about the device, like "rattling" buttons, a protruding SIM tray, and quiet, muffled volume through the device's speaker. It's worth noting that not all units faced these kinds of issues, but it's pretty clear that there were enough for Google/LG to step in and make some changes.
Shinral also noted that the newer revision's display has more of a yellow tint, though it's unclear whether or not LG is using a completely different display moving forward or if the particular unit in question just happened to be slightly unbalanced compared to other models.
Either way, there's a good chance that anyone who ended up with a "defective" Nexus 5 will end up with this newer hardware revision should they choose to return the original.