Here they are as columns. Less similarity (one blue, two red, no common cmyk values or whatnot), but still worth a try:
I agree with simple = better, and dividing them as such could be a red herring. Right now I’m just throwing lots of poo at the wall and seeing if it sticks 
reading the color hexcodes from right to left instead of left to right (this is a Japanese learning website after all) results in two blue colors and one black.
Top → Down = 2 x pink 1 x black…
Look at the image for the badge Ghost of Crabsmas Durtle
Let’s forget about hexdec then for a minute and go back to the drawing board. They’re pairs of digits, 9 pairs of 2 digits, what do they have in common? A letter and a number? (Not in the case of AC, assuming hexdec is out)… So what else do they have in common?
They are symbols
They are white
They are in a box
They are ordered in a sudoku style
They are orderes as a matrix
They have the same font ( can somebody check the actual font?)
I’ve been trying that since yesterday, but no luck so far.
Hah. I was just about to say that.
More of a magic square than a sudoku. It’s not a magic square, though.
I toyed with the matrix idea but it didn’t relate to them being common in any way, because in a matrix the whole is important but not the individual parts… so much.
Vectors maybe?
Calcrostic? Alphametic? 
I thought of RGB colors almost right away, but I’m thinking grouping the givens together is the wrong way. It says what do these nine pairs have in common, not these groups.
Vectors in what context?
I have the book, but it’s a new version so probably not it. Getting the right version of the book would be such a crucial point i doubt that is the answer (and yes, I have tried all combinations of “the answer” too 
)
I bet they are laughing hard at how complicated we are thinking, and the answer will be stupidly easy when we find it 
If all this is providing any entertainment to the folks in the office over the Christmas then I’m glad for it
I want to help but I’ve already used all my ideas 
I’m not smart enough for this lol
PLOT TWIST
It’s impossible and the Tofugu team is tryna see how many people they can confuse at once
Same
I’m doing background research (and hoping the answer just pops in my head while I’m not trying as hard)
Escape rooms are fun :DDD Except whenever I go with my sister I do all the work and she takes the credit … -.-
I still think it’s awfully suspicious that they are hex values though… My first thought will always be colors when it comes to them.