I don't this quite answers your question, but I hope it does.

The development of a language is really a large thing, but I have an example in French which still influences how Francophones write today.

I know if you can count it as a mistake per se, but the French word Nénuphar, also written Nénufar, was an adaptation of a word taken from medieval Latin, but initially from the Persian language.

The ph letters are attributed normally to Greek inspired words, like Philosophie. The ph Nénuphar stood its ground and still does, even though the major language instances in the French-speaking world nowadays prefer to honor its roots by recommending to write with an f : nénufar.

And like many things in French, it complicates the learning of the language. Yet again.

Hope it helps.

David Crystal's book Spell It Out has a wealth of information on the topic as regards the English language. Recalling that info, I think the answer is that scribal errors would often become canonical, because they'd be duplicated by other scribes, and then the words pronounced based on this erroneous spelling, together with compound words that include it, etc. There is also a movement towards separating homonyms both orthographically as well as, eventually also in pronounciation in order to eliminate ambiguity.

All this said, I would guess that the low rates of literacy in ancient and medieval times would mitigate the propigation of such errors and influences.