A recent article has given me some insight as to why not to leave your discs in the console. Most of the reasoning behind it is common sense but you wouldn't expect anything to happen to your disc while its in there.
Along with the most common reasons being that the consoles collect a lot of dust to spread around the disc but other than that they generate a lot of heat that has a chance to mess up the data on the disc. Another reason is that over time is the disc isn't in a upright position it can warp over time into an unreadable disc.
I have left my disc in my console for months at a time and have noticed scratches started to appear on them, so in my opinion it's better that we don't leave them in the consoles and return them to the disc case.