It's the case everywhere, it's due to the first years/contracts that rarely match your actual worth and that includes Messi. Messi at 18 years old was arguably the best player in the world but he wasn't paid like the best and his renewal in 2008 showed that with a very big increase. What you need to consider is how much money clubs spare by paying a players what amounts at several dozens of millions under market for example if you pay 17-20 years old Messi 10m instead of 15m per year, you spare 15m, either the player realizes it and ask for a big signing bonus or he let it slide.