This works both ways; your questions phrasing assumed that the person you responded to felt the same way about how quotation marks should be used. It seems likely that you knew the answer was that they weren't intending to literally quote anyone, but you didn't ask them about that first, which is why it comes across as passive-aggressive.
For clarity, this is the comment that the quote was referring to:
> The comment you are replying to makes so many mistakes about how Testcontainers works on Java that I'm not sure what source code the commenter is looking at.
The comment quite literally calls something wrong ("The comment you are replying to makes so many mistakes"), and it doesn't give any evidence to the claim that there are "so many mistakes" to explain this. When someone says one thing and then claims that it shouldn't be taken literally because they intended something entirely different, that's called gaslighting.