Learn English – Quote about making simple things complicated and complex things simple

In your first query, the question mark clearly does not belong to the euphemism, so it should not appear inside its quotes:

“Why should I ever hear about this... ‘agency’?”

In your second query, you can dispense with the exclamation mark. While that does go with the word Stop, it isn’t heard and doesn’t need to be quoted. And the final full stop isn’t needed either — you’ve already conceded that right at the start.

He screwed his eyebrows, and asked, “Are you sure you heard ‘Stop’?”

Punctuation is only there to assist understanding. Too much clouds the meaning because although it might be strictly correct, it requires working out! Use enough to make the meaning clear without undue effort sorting through it all.

The short version is: Use quotation marks only if you are quoting someone's actual words. If you are not quoting someone's actual words, do not use quotation marks. There is no parenthetical you can add to correct for this.

In an apocryphal quote, you are quoting the actual words that are attributed to the person; for example: "I cannot tell a lie" can be quoted and attributed to "George Washington (apocryphal)". If there was a definite source for the shortened version, you could list that person's name: "Play it again, Sam" could be attributed to "Woody Allen (paraphrasing Humphrey Bogart)".

But if the paraphrase is not part of someone else's quote, you can't put it in quotation marks; in formal writing, this will be seen as sloppy; in academic writing, dishonest. Instead, you need to put it in a sentence. "Abraham Lincoln said that we got here eighty years ago" is appropriate. "We got here eighty years ago." --Abraham Lincoln (paraphrased) is not.

Depending on the specific quote you want to use, you might be able to get away, in informal writing, with an (attributed). For example: "Play it again, Sam" -- attributed to Humphrey Bogart. Who it's attributed to him by can remain unsaid. Or, if the paraphrase is close enough, you may be able to "fix" it with brackets and ellipses: "Play it [again], Sam."

But much as I hate to say it, the best solution is to use a different quote. Consciously perpetuating a misquotation, no matter how you dress it up, will lead to mistrust in your audience.