Perceptual grouping is the process of organizing sounds into perceptually meaningful elements. Psychological studies have found that tones presented as a regular frequency or temporal pattern are grouped according to gestalt principles, such as similarity, proximity, and good continuity. Predictive coding theory suggests that this process helps create an internal model for the prediction of sounds in a tone sequence and that an omission-related brain response reflects the violation of this prediction. However, it remains unclear which brain areas are related to this process, especially in paying attention to the stimuli. To clarify this uncertainty, the present study investigated the neural correlates of perceptual grouping effects. Using magnetoencephalography (MEG), we recorded the evoked response fields (ERFs) of amateur musicians and nonmusicians to sound omissions in tone sequences with a regular or random pattern of three different frequencies during an omission detection task. Omissions in the regular sequences were detected faster and evoked greater activity in the left Heschl's gyrus (HG), right postcentral gyrus, and bilateral superior temporal gyrus (STG) than did omissions in the irregular sequences. Additionally, an interaction between musical experience and regularity was found in the left HG/STG. Tone-evoked responses did not show this difference, indicating that the expertise effect did not reflect the superior tone processing acquired by amateur musicians due to musical training. These results suggest that perceptual grouping based on repetition of a pattern of frequencies affects the processing of omissions in tone sequences and induces more activation of the bilateral auditory cortex by violating internal models. The interaction in the left HG/STG may suggest different styles of processing for musicians and nonmusicians, although this difference was not reflected at the behavioral level.