Thematic analysis is a methodology with wide use in content analysis and field work through interviews, observations, and focus groups. Despite popularity with researchers, there are several questions and problems with the methodology. There was an absence in exploration and explanation of the methods and hidden steps in thematic analysis. Using a case study with a thematic analysis of the methods of thematic analysis and an autoethnography, issues and concerns were examined across a broad sample of articles published using thematic analysis. Seven major problems permeate thematic analysis research, and recommendations to improve thematic analysis and all qualitative research are presented.