At the Straits of Messina, the tunnel would be crossing an active rift zone ( https://en.wikipedia.org/wiki/Siculo-Calabrian_rift ). That rift is the source of those big earthquakes - such as https://en.wikipedia.org/wiki/1908_Messina_earthquake - which was at the Straits, magnitude 7.1, and killed ~75k people. And for extra bonus fun - https://en.wikipedia.org/wiki/Mount_etna - is one of the world's most active volcanoes, part of that active rift zone, and less than 80km from the Straits.

(Vs. the geological maps I can find seem to show that the Seikan tunnel does not cross any sort of active fault.)