There were several misconceptions I had about Sanatana Dharma:
• I thought all Hindus accepted Chaitanya Mahaprabhu and Ramakrishna Paramhamsa as incarnations of Vishnu. It was only later I found only Gaudiya Vaishnavas and followers of Vivekananda considered them as incarnations of Vishnu.
• I thought Jivatmas originate from Brahman. It was only later I learnt that almost all Hindu sects believe that Jivatmas are never created.
• I thought Upanishads were seperate from the Vedas. It was only later I found Upanishads were parts of the Vedas along with Brahmanas, Aranyakas and Samhitas.
• I thought all Hindus except ISKCON saw Krishna as an incarnation of Vishnu. It was only later I learnt that all Gaudiya Vaishnavas along with Nimbarkites and Pushtimarga Vaishnavas saw Vishnu as an incarnation of Krishna.
• I thought that the Hindu scriptures only mention ten incarnations of Vishnu. It was only later I found that Hindu scriptures mention more than ten incarnations of Vishnu.
• I thought there was only one type of Moksha- Salokya. It was only later I learnt that they are other types of Mokshas- Kaivalya, Sarupya, Sampiya and Sarsti.
• I thought only Brahmanas had the right to undergo Upanayana (that's what happens in Bengal). It was only later that I found that even Kshatriyas and Vaishyas are eligible for Upanayana.
• I thought that the Puranas were highly unreliable since each Purana had a different version for the same story. It was only later I found that each of the Puranas correspond to a different Kalpa where the same event occurs with slightly varying differences.
• I thought the term "Devas" translated as "Demigods" in English. It was only later I learnt that only except ISKCON, nobody saw the term "Devas" to be translating to "Demigods".
Whew! There might have been more misconceptions which I can't remember right now. Will add them once I recall.