It seems strange that your bike would only squeak after riding it for a while. After all, it’s not like you are installing a new part while riding. However, the bike does change a little bit. Many materials expand when they heat up, and that could increase friction, and subsequently, noise.
Of course, the engineers who designed your bike were aware of such things, and constructed your bike to be noise-free. The same is true for the engineers who invented railroad tracks. If you didn’t know any better, you might think that tracks are nailed to the crossties, but they are not. They are attached with clips to allow them to move when they get hot. Take a look at this photo:
I once had a mysterious squeak on my mountain bike. Flipping the bike over and spinning the back wheel resulted in no noise at all. In fact, the wheel spun perfectly – seemingly forever – like a perpetual-motion machine. But after riding it for a couple of miles, it would heat up and everything would change. The bike made so much noise that people would stop and turn their heads to look at the ne’er-do-well disturbing the peace.
I solved the squeak by inspecting my wheel hubs. I was surprised to find that the drive-side rear axle was covered with what looked like a fuzzy, black caterpillar. When I poked it with my finger, it turned out to be a blob of grease. So, the seal had failed and the grease leaked out.
Further reading: search on “baring heater” and you will find machines that heat up bearing assemblies so that they can be fitted onto a shaft.