It's bad sign, it's a sign that they are not comfortable. Mine have very good polyp extension all day long, all night long. At night there is even more polyps out, those at the tip as fully out at night.
Post your water parameters. Also you might want to check your tank for copper. YOu can use polyfilter just to make sure you don't have anything nasty.
How strong is your flow? if it is too strong it might as well affect the extension.
But first you should post all your parameters, salinity mesured with a good refractometer, alkalinity, calcium, mag, nitrates, phosphates etc.
Also what type of light are you using and what acclimatation did you do for the light?
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More fish die from human stupidity than any other disease...
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