Learn English – “I did not see him yesterday” vs. “I had not seen him yesterday”

I think you're overanalysing this one. Obviously native speakers often make "slips" like this, especially in casual conversation or Q&A website comment posts.

In the case of X mistaken for Y, I imagine almost every competent native speaker would say for is "correct", but many if not most wouldn't see anything seriously "wrong" with as. A (probably, much smaller) number might not see much wrong with with.

This is an example of a comparatively minor slip. On a site like ELL, for example, many users are native speakers, and many aren't. As it happens, we have contextual information for the specific comment that sparked this question, making it highly likely that the writer is in fact a native speaker. But even if there were no such evidence, the fact of the usage itself would be no real reason to suppose otherwise.

This shouldn't be taken as a general principle for all "misused" prepositions, etc. Some errors are far less likely from native speakers, and far more likely to be seen as "giveaways" indicating "non-native".

I didn't see him yesterday

is a more standard way to express the basic idea.

I never saw him yesterday.

We would normally use never saw in this way only when there is a special reason to do so.

As Adam and gnasher729 point out or suggest, the reason for doing so is to communicate contrast.

For example, many prior occasions contrasted with none

Although I saw him several or many times before yesterday, I saw him zero times yesterday.

Or a lengthy period in which I might have seen him or numerous opportunities to check or notice contrasted with zero sightings

I was here all day (or I looked for him many times) but in all that long period (or on all those many occasions) I didn't see him even once.