Not sure why, but if you don't do your ship ability challenges until after your guild reset then they will count towards your daily challenges for the day (which is cool). However for some reason ship building materials (under ship challenges) doesn't count against the daily challenges.
It's not a big deal, doesn't hurt anything, just found it strange and wonder if anyone knew the logic behind it (and to clue in those that didn't know).
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Yes, they do. I have no idea what the OP is talking about.
I think k he may be confused the capital ship challenges don't count towards challenges because they are one and done at each tier. The ability and building material challenges do count.