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It's probably because you did not start from a transparent document as shown at the start of the video. When you start from a transparent document and do the "Define Pattern",  the pattern will be saved without the background(that is without white in this case).

If you have started with a white document, when you do the clipping mask with the solid color it will show up as a whole(like the problem you are getting now) instead of showing up at only the patterns.

So, I would suggest to start the "pattern making" ( from 0.22 to 2:10) again with a transparent document (follow it exactly for now) and come back to the second document and try the clipping mask again. It should work!