I'm having exact same issue as in this github thread
(I don't know what pdf convertor Calibre uses anyway, but issues are identical):
https://github.com/wkhtmltopdf/wkhtmltopdf/issues/2422
I'll also use their text to describe it: "When a hyperlink (<a href...>) spans a line, clicking anywhere in either of the lines will activate the link."
Calibre version: 5.27
Below is screenshot with my mouse pointed outside of links (actually my Lightshot app failed to capture mouse pointer itself, and I'm indicating it's position with an arrow)
And below are example .epub file, pdf job details and output .pdf file
LinkLineSpan.epub
link_issue.txt
Link line span example - Unknown.pdf
It's not critical, but I'd like to deal with it
(and of course thank you for excellent tool!)