It happens to the best of us.
"Stay the course," for example, just meant to "finish," "stay until the end (of the race course)" Rather like "stay the night" just means "stay until the end of the night." Somehow it came to mean "fix the course", i.e., the intended path or the plans. Bush II was older. Newsfolk were younger or less acquainted with the expression. It gave me a headache until I sorted out how the newspapers and young'ns got it wrong.
A lot of the confusion in your list results from homonymy. "Deep seated," with flapping, leads to "deep seeded." Same for most of your examples--a bit of laxness in articulation and there's (near) phonetic merger, with phonemic merger not far behind. My dialect of English sounds stilted. We don't flap normally (we also have Canadian raising--I'm from Maryland, south of the Mason-Dixon line, not north of the Canadian-American border).
Left-of-center folk also fall prey to the problem. "Squaw" was a big no-no, when it's originally not offensive (or, if so, offensive only in a particular variety of one language). Then again, a lot of people like to use language as a cudgel; if they like to view themselves as maternal, it leads to the impression of wannabe child-abusers ("I"m the nurturing mother figure, come here so I can cudgel you and shove peas into you."
A lot of expressions have less-than-reputable sources. "Feel blue," "bend over backwards," etc. "Keep on trucking" is usually a shocker. My mother would say, "Keep on trucking" and I'd reply, "Ma, that was originally 'Keep on fucking'." "What did you say?" "You said it first. Did you really mean it?"
Others are just different from their original form. "Lord" was "loaf-ward", the guy who handed out the bread to the day laborers/serfs on a manor. Sort of makes "Give us this day our daily bread" into a kind of cross-linguistic pun--"the bread-warden's prayer" (it had no such meaning in Greek or Hebrew). "Starve" just meant to "die," having no specific cause in mind.
Others are misattributed. "Robin" is a European bird, not the American red-breasted variety. "Guinea pig" is neither a pig nor from Guinea.
Let's not even get into syntactic change. The confusion of "less" and "fewer" for mass/count nouns. Or the failure of NEG-raising, having negation occur before a quantify. "Everybody did not go to the concert" is far from meaning "Not everybody went to the concert." In the first case, nobody went, under a neutral, non-accented pronunciation. Among younger speakers this usually means most people went--which is what older Americans interpret the latter example to mean.
My dialect of American English preserved the subjective. Everybody said "It is important that Fred be at the meeting" if the meeting wasn't actually occuring at the time. "It is important that Fred is at the meeting" asserts Fred is currently at the meeting and his presence is key. This distinction is pretty much lost. It trips me up every time I find educated newsfolk failing to observe traditional norms wrt the subjunctive. (My kids tend to think I'm getting African-American Vernacular English wrong--"be" would be habitual or durative in that dialect, and for a since instance there'd be a zero copula.)