For example, I had a battery become unusable because Linux often failed to sleep when the lid was closed because some dialog box was blocking. It would run in the bag with no ventilation when I didn't realize it until the battery drained and it would fail to shutdown until the hardware fail-safes took over and I realized my backpack was too hot to hold. Did this a few times and the last time, the battery wouldn't charge anymore. After getting a new battery I became very conscientious about whether it actually was asleep before I put it in the bag.
I have had this happen in Windows before as well, in one case it would wake up if I forgot to turn off my Bluetooth mouse when I put it away. Since it was already closed, there was no trigger to go back to sleep so it would run itself dead in the bag and eventually the plastic near a hot component melted. Turns out there is an option in the Windows device manager to tell it not to wake on Bluetooth that prevents this.
However a defect in the factory-installed operating system that causes failure is something you have to warranty. A defect in the user-installed operating system is not. However, I have no idea how they could trace the problem to the operating system. Not sure how they would ever know that Linux is installed. Any good Linux user would wipe the hard disk before returning a computer to the manufacturer for repair :)