I used to believe that embryos pass through periods of development representing earlier evolutionary stages
The way you stated it is actually not wrong, especially if your use of "representing" means "looking like". What is wrong is the much stronger statement that follows, "basically a fish", as opposed to, say, "human embryos pass through a stage where they have slits in their necks resembling gills, though without the same function". I suspect that this is closer to what your father meant.
What is something you used to believe, preferably something concrete with direct or implied predictions, that you now know was dead wrong. Was your belief rational given what you knew and could know back then, or was it irrational, and why?
Edit: I feel like some of these are getting a bit glib and political. Please try to explain what false assumptions or biases were underlying your beliefs - be introspective - this is LW after all.