Background: Effective emotion regulation should be reflected in greater coherence between physiological and subjective aspects of emotional responses. Method: Youths with normative to clinical levels of internalizing problems (IP) and externalizing problems (EP) watched emotionally evocative film-clips while having heart rate (HR) recorded, and reported subjective feelings. Results: Hierarchical linear modeling revealed weaker coherence between HR and negative feelings in youths, especially boys, with more EP. Youths with IP showed coherence between HR and negative feelings that did not match the affect portrayed in the eliciting stimuli, but atypical positive emotions: they felt happier when they had slower HR. Youths without problems predominantly showed normative emotional coherence. Conclusions: Youths with EP and IP experience atypical patterns of activation across physiological and experiential emotion systems which could undermine emotion regulation in evocative situations.