There is general say that too much everything is bad including too much sleeping. When it comes to sleeping, moderation is always the watchword. With this said, if your waking up is due to over indulging in sleeping, I will say yes that waking up late can make one to be overweight. Let's say for example you slept by 9pm and you woke up by 9am. As you can see you've over slept. And this pattern of sleeping leads to fatness.
Another scenario is when you don't have enough sleep. If you don't sleep well you could be become prone to overweight. Maybe you are the type that sleeps very late and wake up very early. Or you are the type that sleeps very early and wake up too very early, meaning sleep you had wasn't enough. Cases like these could also lead to overweight due to not having enough sleep.
Point worthy of noting is that you are expected to sleep 6-8 hours per day regardless of whatever you are into, and if its above this time, it's sleeping over done, and if below it's sleeping not enough. Both of them have propensity of making one fat.