Google has just added an interesting page to the Nexus support site that lists new operating system safety warnings. According to the page, this is a boot verification system that checks the integrity of your device software during each startup. You probably haven't seen this on any devices yet, but Android M is right around the corner.
There will be three different error messages associated with the verified boot system. If you see a yellow exclamation and "Your device has loaded a different operating system," that means you have an unofficial ROM of some sort installed. If this is your doing, no problem. The orange warning icon means that your device can't be checked for corruption. This happens because the bootloader is unlocked. You can lock it if you want, or just ignore the message. Finally, there's the red symbol, meaning "Your device is corrupt. It can't be trusted and may not work properly." This could still be the result of some change you intentionally made, but the verified boot system isn't liking it. Alternatively, something has gone horribly wrong.
All these messages will go away after 10 seconds, or you can press the power button to bypass immediately. The support page doesn't go into detail about the technology behind Android's operating system safety warnings, but it's probably based on dm-verity, which was added to Android in 4.4. It hasn't been surfaced as a user-facing feature, though. The addition of the boot warnings seems to indicate that at least Nexus devices will have boot verification front and center in Android M.
- Nexus Support