The Timer System Control Register is the key register to deal with. It also controls how the timer system operates in various modes such as Background Debug Mode, WAIT state, and also how the timer flags are cleared. Its an option available to you. If debugging your program is being very timing dependent, you may be able to debug the problem. Might be useful, might not.
Lets move on.
To confuse things a little bit, there is a prescalar register that allows you to change the relationship between MCLK and the TCNT register. The only states that stop the clock are Wait and Background Debug Mode. The prescalar is a useful tool. The prescalar allows you to control the amount of time it takes for a single increment of the clock. By default, the prescalar is set to 1 on reset, which means the TCNT register is incrementing at the MCLK speed.