Pathological speech analysis with Automatic Speech Recognition (ASR) is a long-standing research domain based on the expectation that there is a close relationship between pathological speech abnormalities and reduced ASR performance. This has led to interest in ASR-based clinical analyses such as intelligibility assessments and disfluency detection. However, these analyses are premised on transcriptions that accurately reflect abnormalities. We find that the choices of ASR model and speech task significantly affect transcription errors for both typical and pathological speech, which is reflected in the word error rate (WER). Notably, language restriction (e.g., dictionary of words) decreases a model’s ability to capture abnormalities while more complex tasks increase both model and speaker-driven transcription errors. These findings highlight possible variability in clinical analysis with ASR and suggest the importance of controlling for model type and task complexity.