Deliberate mistake: As the Lotus drives off the pier and enters the water, the exposed underbody is that of a normal car. After it enters the sea, the underbody we see is completely sealed, which it needs to be to allow the car to submerge.
Deliberate mistake: When the speedboat docks at the Stormberg Laboratory with Bond on board the speedboat has no helm or gauges fitted to the dashboard. From that angle we should see them or something resembling them as we did when Bond was picked up.
Chosen answer: When the nuclear subs have been destroyed, there's an explosion in the control room, and one of the men cries out "Fuel tank!" Liparus has numerous internal fires raging after the battle with her crew. These uncontrolled fires eventually spread to her fuel tanks and ammo storages, one of which explodes in a huge fireball and finally causes Liparus to sink.
I thought the final explosions that sank the Liparus were deliberate self destruction after completing the mission in an attempt to destroy any evidence, rather like when Bolfeld manually triggers explosives after being thwarted in You Only Live Twice.
Liparus sinks slowly, and that would leave her crew plenty of time to evacuate. Angry and armed crew with a grudge against Stromberg.
Jukka Nurmi