Clipping typically occurs in the audio hardware when an analog signal is too loud and therefore converted to digital in the A/D converters of the hardware.
Clipping can also occur when the signal from the input bus is written to a file on your hard disk. The reason for this is that you can make settings for the input bus, adding EQ, effects, etc. to the signal while it is being recorded. This may raise the level of the signal, which causes clipping in the recorded audio file.