I'd say it is a circulation problem rather than some contaminant or adding fish too quickly. If your corals were not affected and the fish were fine during the day it has to be the difference between the daytime conditions and night time.
During the day, the photosynthetic corals and macroalgae are undergoing photosynthesis where:
carbon dioxide + water ---> glucose + oxygen
So during the day oxygen levels are high and the fish are happy.
At night, the reverse is true and the photosynthetic organisms are undergoing aerobic respiration using up the sugar they produced during photsynthesis:
glucose + oxygen --> carbon dioxide + water
So your corals and macroalgae are now competing with your fish for oxygen. As well, the carbon dioxide is converted into Carbonic acid and the pH drops.
So your fish become stressed and may even suffocate and die.
I would imagine your flow at night is not agitating the surface water and getting oxygen to the bottom of the tank where the gobies live. I don't think I've seen gobies go to the surface to try to gulp down air and even if they did, they would sink back to the bottom.
Re-aim your powerhead placing near the surface to force water down to the bottom or at the bottom to move water to the surface. I bet it is just flowing linearly parallel to the surface.
Or add more flow with more powerheads.
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