Yes, I believe they were indwelt by the Holy Spirit! The only example I can find in the Scripture where people were baptized by water and later on Paul baptized them with the Holy Spirit, it refers to people who had heard the teachings of John the Baptist. They may have heard something about Jesus, but they were baptized with John's baptism, i.e. a water baptism. As soon as they were properly taught and they believed in Jesus, they were baptized with the Holy Spirit.
Was his baptism effective or is it possible they may need another one?