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Have you checked them for accuracy, though? What type of thermometers?

40% should have been fine for incubation. I incubate dry so often lower than that. Are you using a calibrated thermometer for your temps? If you're having so many late hatches I think your temperatures are too low.

Yes, you can candle if you want. How were you monitoring temperature? Is it a still air or forced air incubator?

Chickens or ducks? Chickens take 21 days so something may be off. What temp were you incubating at? They are already two days late so I'm thinking your temperatures were too low or they're already quit.