You'll either need to do 1 of 2 things:
1) Change your GLOBAL shape parameters to allowing "small" shapes to fill. The design has little shape areas and your GLOBAL shape parameter is set to disregard shapes under 'xx' size.
2) Select each shape at the X-Y locations shown, and set the fill size parameter to allow filling these small shapes.
I've done both before, so it's up to you to decide which will work best.