I’ve always thought that nugatory should mean “the creamy chocolate center of hell.”
I have to consciously remind myself that vermilion is not a shade of green, and that chartreuse is not a shade of red.
And then there is “cleave” which can mean either separating or sticking together. Jeez.
Specious.
This can bring to mind several things, all of which are probably not related to the word at all.
Restive.
Impassive.
Impregnable.
Fulsome is I word that I see misused frequently, (much to my amusement).
And me for surfeit
The word is slowly returning through misuse to its original meaning 
Crapulent.
Nonplussed confuses me. “Jim was totally nonplussed by the news his mother was a cannibal” seems like it should mean “he seemed unbothered/unmoved” when of course it means he’s disturbed and speechless.
Nauseous seems like it should mean “sick” or “sickened” rather than “to make one sick” (which it seems nauseated should more than cover) while noisome should be a noun having to do with knowledge, not an adjective having to do with disgusting. “The noisome left him nauseous” sounds better than “The noisome smells of Jim’s mother’s cannibalism left him nauseated.”
should read "having to do with noise.
“Hopefully” is a word that works better as it is used rather than how it is actually intended. “Hopefully I will find an appendix donor for my wombat tomorrow” does not mean “I hope that I will find [etc.]” but rather “Tomorrow I will find [etc.] wombat and when I do I will have hope”. I think the meaning should be switched to the vernacular rather than the official.
For the longest time I kept confusing “niece” and “nephew.” Nephew just sounds so feminine to me.
And “levity.” It sounds heavy and serious, like “gravity.”
And of course “hoi polloi.”
I used to think that superficial meant something like superlative. So that if you had superficial hearing you were like Superman or something.
Enervate. It sounds to me as if it means ‘energising’.
Scurrilous sounds like it has to do with small mammals hurrying around. Instead, it means false and insulting. (Tom was peeved by the scurrilous “won’t come out of the closet” scene in South Park.)
Scrofula has always sounded kind of dirty to me.
And I keep thinking fecund has something to do with shit.
When I was learning all the names for family members in English I kept calling my cousins my nieces and nephews. How are you supposed to tell if they’re boys or girls if you have the same word for both? (I later found out that the answer is “you can’t”.)
Afflatus doesn’t sound like a “strong creative impulse, especially as a result of divine inspiration”.
We have a visiting priest who regualrly exhorts us to “pray for a fulsome faith”. I was going to let him know about this until I read the usage note at dictionary.com (bolding all mine): “Fulsome is often used to mean “offensively flattering or insincere.” But the word is also used, particularly in the expression fulsome praise, to mean simply “abundant,” without any implication of excess or insincerity. This usage is etymologically justified but may invite misunderstandings in contexts in which a deprecatory interpretation could be made. The sentence ‘I offer you my most fulsome apologies’ may raise an eyebrow, where the use of an adjective like ‘full’ or ‘abundant’ would leave no room for doubt as to the sincerity of the speaker’s intentions”
I guess I can assume that the context of what he was saying is clear so I have to let it go.