Depending on the email messages in question it could be related to
`mu4e-view-html-plaintext-ratio-heuristic'.
By default, mu4e will show the HTML part if the text part is "too short"
relative to the HTML part, based on a simple heuristic. This is the case
even if you set `mu4e-view-prefer-html' to nil.
To override that and always show the text part when available, you can
add this to your init file:
(setq mu4e-view-html-plaintext-ratio-heuristic most-positive-fixnum)
Hope that helps
John