John Gill Commentary Numbers 9:16

"So it was alway: the cloud covered it, and the appearance of fire by night." — Numbers 9:16 (ASV)

So it was alway
Night and day, as long as the people of Israel were in the wilderness, see (Exodus 13:21Exodus 13:22) (Nehemiah 9:19) ;

the cloud covered it [by day] :
the phrase, "by day", is not in the text, but is easily and necessarily supplied from (Exodus 40:38) ; and as it is in the Targum of Jonathan, and in the Septuagint, Vulgate Latin, Syriac, and Arabic versions, and which the following clause requires:

and the appearance of fire by night ;
when as a cloud it could not be because of the darkness of the night; as in the daytime it could not be discerned as a body of fire or light, because of the light of the sun; but being seen under these different forms, was serviceable both by day and night, for the following purposes.