Deep learning has shown promise in decoding brain signals, such as electroencephalogram (EEG), in the field of brain-computer interfaces (BCIs). However, the non-stationary characteristics of EEG signals pose challenges for training neural networks to acquire appropriate knowledge. Inconsistent EEG signals resulting from these non-stationary characteristics can lead to poor performance. Therefore, it is crucial to investigate and address sample inconsistency to ensure robust performance in spontaneous BCIs. In this study, we introduce the concept of sample dominance as a measure of EEG signal inconsistency and propose a method to modulate its effect on network training. We present a two-stage dominance score estimation technique that compensates for performance degradation caused by sample inconsistencies. Our proposed method utilizes non-parametric estimation to infer sample inconsistency and assigns each sample a dominance score. This score is then aggregated with the loss function during training to modulate the impact of sample inconsistency. Furthermore, we design a curriculum learning approach that gradually increases the influence of inconsistent signals during training to improve overall performance. We evaluate our proposed method using public spontaneous BCI dataset. The experimental results confirm that our findings highlight the importance of addressing sample dominance for achieving robust performance in spontaneous BCIs.