Is there any way to capture this specific city?

This city is surrounded by districts on 3 sides, water on 2 and a temple on the last. Autopathing on an attack loads my army into a boat that just sits off the coast because they can't land. Is there anyway at all to capture this city?

I don't think you have to attack the "city center" tile itself to engage in an attack on the city - I think, as the hero standing there, that it would suffice to attack the borough tile, and that would initiate a combat against the city.

However, as you're suggesting there are definitely some serious bugs in their random-map-generator, mostly due to the whole way they've designed embarking, and the lack of water combat - which result in inaccessible strips of land trapped behind a single ruin/village - which is most problematic when it literally prevents you from doing a crucial quest (there will often be a minor-faction-unit stuck back there, sitting on a single tile you can't disembark onto because it's already occupied).

There's also just a general design flaw in the way that coastal edges of a city are not attackable - if you get a small city on an island, and perfectly fill the whole island, it's impregnable because there's nowhere to disembark.

You're not the only person to run into this - so if it looks like a bug hosing your ability to do something, it just might be.