This has been driving me bonkers but I think I finally figured something out.
I drew the top outer triangle on graph paper showing millimetres with a fine pencil, then starting in the bottom right corner put in the other shapes, the bottom light green one 2cm tall on the right side, then the orange one above it 1 cm tall.
The top left corner of the orange shape does not in reality intersect with the angle of the outer triangle but sits 1mm below it. Given that the top green triangle is 5cm wide, that accounts for half of the 'empty' square in the bottom diagram.
Not sure where the other half comes from, maybe my fine pencil is not fine enough and there is actually a 2mm gap?