The mind is a junction of consciousness, subconsciousness, and super consciousness. Whatever thoughts occur in our minds live in the subconscious zone. While meditating, the mind is relaxed and calmer than before. There are no voices, continuously interrupting us. Thus, it is understandable that the thoughts that were suppressed in the subconscious earlier could hit back.
If you're searching out for the purpose of mediation, check: How does meditation help in beating everyday tension?
And anyways, meditation is an exercise done to increase awareness toward increased awareness. So, there is nothing wrong with facing the thoughts in the super relaxed zone.