A brother prayed Asr congregation in the Masjid with us and then this brother helped a person who missed the congregation by making their own congregation intending that it will be his Nawafil. Does this not go against the Hadith that there is no prayer after Asr until Sunset?

‎No. Shaykh Ibn Uthaymin said a prayer that has a cause is not prohibited after Asr, and the prohibition is on general voluntary prayer, so praying with someone who missed the congregation as charity to him is fine. The Prophet ﷺ‎ saw a man praying alone and said, "Will no one give charity to this man and pray with him?" (reported by Abu Dawud; graded sahih by al-Albani raḥimahullāh).