I know of 3 major issues on qualitative research:
- measurements (coding) of values (of variables) -different biases give incorrect data, same code for different values or different codes for same values;
- statistical tools used to derive deeper analyses -often wrong tools are used because the conditions for correct use are not follow rigorously (the underlining assumptions are not properly considered in selection of tools); common examples are treating discreet variables as continuous variables (with numeric coding for groups);
- researcher’s bias and preference, often guide results to certain presumption or conclusion that fits apparently safe outcomes for the researcher.

In sum, qualitative data, qualitative methods, and qualitative research have issues.