Why do many uC have more then one I2C interfaces?
As @JohnD says, you may need to talk to several devices which have the same built-in, unchangeable address.

Another reason for multiple I2C busses is that they can be very slow. Standard I2C devices only run at 100 kHz. By having multiple busses you can access multiple devices in parallel, effectively increasing the data rate.

A third possibility is that you want your MCU to act as a slave on one bus and a master on another.