When a city you want to attack is underwater (and no tunnels around it)
The mechanics of the game bug severely.

any hints how to fix them are helpfull

I tried per transport type and here is the buglist :

Bug 1 : attacking/bombing with airplanes ( Tested : fighter, bomber, interceptor, stealth fighter, stealth bomber) works on deep sea city's
This should not work since ocean city's cannot build airports (they are supposed to be submerged remember)

Bug 2 : Attacking/bombing with ANY naval unit works
(Tested : destroyer, battleship, PT boat, scout sub, sub, nuclear sub, plasma destroyer, kraken, moray striker, dreadnaught, ironclad, shipoftheline, aircraft carrier, fire thireme)
This should not work on all these units, since ocean city's are supposed to be submerged.
(Battleship, ironclad, shipoftheline, aitcraft carrier, fire thireme, destroyer, plasma destroyer should certainly NOT be able to attack ocean city's)

Bug 3 : attacking from crawlers does not work by any unit
While crawlers are MADE to deliver units to such city's it is impossible to attack from them, no matter what unit you place inside them, not even marines
it IS possible to unload them (in the middle of the ocean??) and use them to bombard.
Clearly this is a MAYOR bug, any plugin around that fixes crawlers?

Bug 4 : paratroopers used to capture
The only land-unit in any transportvessel I found able to capture ocean city's happend to be the paratrooper, from inside a helicopter.
Like Bug 1, this should not even work!