fugal infection

You didn't mention how you incubate the eggs after fertilization. Incubation temperature is very important for embryonic development and for parasitic control you should use something like salt, Iodine or some chemical.  

it is critical that preparation before spawning induction follow a set of simple protocols and one of which is to ensure that the clams shells are scrapped clean of any algae and fungus before commencing the spawning induction process. This may reduce introduction of parasites into your incupation tanks.

Thank you for sharing those valuable information. For your information, the incubation temperature for the fertilized eggs was set up between range 23 to 25 degree Celcius. The tank containing the fertilized eggs was kept in the dark room.

I really hope that any individuals that had experienced doing research on bivalve culture could share their knowledge with me. 

bivalve hatchery need a high standard of hyigene like any other species. This is the first principal. All equipment used must be clean and not contaminated by other activities. water used for spawning induction must be screened well with a clean mesh to stop parasites in the water systerm to enter the larval rearing tanks.

Besides fungal infection, many of the eggs are damaged due to bacterial infections too. 

Some factor impacted to the larval rearing, you have to make sure that the clean water for fertilisation, moving the eggs and sperm into filtering waters then make your aeration continually. This way to avoid the fungal and the bacteria.

Good job 

did the sperm and eggs were kept in separate tanks before fertilisation? if so then how much of the sperm was used for fertilisation?.. note that if after fertilisation eggs were not cleaned with fresh clean water then there is a very high chance of bacteria infection pausing greater risk to the fertilised eggs.