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The warning is meant to be shown when "But" is at the start of paragraphs. However, in its current implementation, it seems to check for "But" at the beginning of each new line in the body of the text. This is incorrect for formats that normalise white spaces and allow semantic line breaks. They can have "But" at the start of a new line within a paragraph (at the start of or within a sentence).
In rst/markdown/TeX, a new paragraph must be preceded by an empty line.
So:
This is a sentence.
But this sentence is not the beginning of a new paragraph.
The warning should not be shown here.
But, it should be shown here.
The warning should appear at the second "But", but not at the first.