Error-based learning is one of the basic skill acquisition mechanisms that can be modeled as a perception–action system and investigated based on brain–behavior analysis during skill training. Here, the error-related chain of mental processes is postulated to depend on the skill level leading to a difference in the contextual switching of the brain states on error commission. Therefore, the objective of this paper was to compare error-related brain states, measured with multi-modal portable brain imaging, between experts and novices during the Fundamentals of Laparoscopic Surgery (FLS) “suturing and intracorporeal knot-tying” task (FLS complex task)—the most difficult among the five psychomotor FLS tasks. The multi-modal portable brain imaging combined functional near-infrared spectroscopy (fNIRS) and electroencephalography (EEG) for brain–behavior analysis in thirteen right-handed novice medical students and nine expert surgeons. The brain state changes were defined by quasi-stable EEG scalp topography (called microstates) changes using 32-channel EEG data acquired at 250 Hz. Six microstate prototypes were identified from the combined EEG data from experts and novices during the FLS complex task that explained 77.14% of the global variance. Analysis of variance (ANOVA) found that the proportion of the total time spent in different microstates during the 10-s error epoch was significantly affected by the skill level (p < 0.01), the microstate type (p < 0.01), and the interaction between the skill level and the microstate type (p < 0.01). Brain activation based on the slower oxyhemoglobin (HbO) changes corresponding to the EEG band power (1–40 Hz) changes were found using the regularized temporally embedded Canonical Correlation Analysis of the simultaneously acquired fNIRS–EEG signals. The HbO signal from the overlying the left inferior frontal gyrus—opercular part, left superior frontal gyrus—medial orbital, left postcentral gyrus, left superior temporal gyrus, right superior frontal gyrus—medial orbital cortical areas showed significant (p < 0.05) difference between experts and novices in the 10-s error epoch. We conclude that the difference in the error-related chain of mental processes was the activation of cognitive top-down attention-related brain areas, including left dorsolateral prefrontal/frontal eye field and left frontopolar brain regions, along with a ‘focusing’ effect of global suppression of hemodynamic activation in the experts, while the novices had a widespread stimulus(error)-driven hemodynamic activation without the ‘focusing’ effect.