Ever since I got my Nexus 5, I've notice that apps sometimes disappear from the launcher for no reason. This seems to correspond to that app being updated, although it doesn't always happen to every app on every update. I've seem some questions about icons disappearing due to moving them onto an SD card, but I don't have one of those so that's not it.
The apps are still installed and show up in
Settings > Apps or in the alphabetized pages one gets by pressing the
::: icon. Some of the apps this has happened to include Facebook, Android IRC, TransitTimes+, QuickPic, and Minecraft — but it's not just limited to those, and it doesn't seem to happen to those with every update.
I'm not using any special launcher or anything — just the stock one that comes with KitKat 4.4 on the Nexus 5. (Updated to 4.4.2)
What's going on and how can I fix it?