Short answer, bubble wrap and layering.
Longer, more detailed answer:
The hexagons are actually the top layer. To get this effect, there's a blended base coat of red and fluorescent lemon yellow put down with intentional streaking of both colors into each other for a nice red/orange/yellow mix.
Then you get some bubble wrap and press it down into your wet paint just enough to get the round impressions but not smear everything. basically that give you spots in your base where the color underneath pops through in a circular grid. If you take the now paint-covered bubble wrap and apply it over another color, you get neat multicolored textures.
Once all that dries, you paint on the hex stencil. I like to vary my thickness when I paint it on so you get some variation between a fully filled in hexagon and just a light wash over your underlying color (again the goal is to give you some color and depth variance and allow your background to pop through).