Why didn't Paul heal Timothy's stomach problem?
Paul did not heal Timothy's stomach ailment because the miraculous gifts of healing belonged to the early church and were not operating in his later ministry. He could no longer heal the sick, so he gave Timothy a remedy and directed believers to pray rather than expect a miraculous cure.
Les explains that the gifts of healing were present in the early church, and Paul himself performed miracles in Acts. But by his later letters there is not a word about those kinds of miracles, and Paul no longer performs them; he cannot heal the sick. Even one of his best friends and fellow laborers was sick near death, and Paul could only tell believers to pray. Timothy evidently had a stomach ailment, and Paul did not heal him—he gave him a remedy instead. Paul's own catastrophes also brought no miraculous healing; the Lord brought him through them. These particular gifts are dealt with only in the letter to the carnal church.