ProBouquet uses a particle simulation to help prevent the flowers and branches from overlapping- while this fixes the majority of intersections, they can't all be avoided. 

In the v1.1 update released 23rd June you'll find a new beta feature for deleting overlapping geometries. This is a little heavy computationally as it involves creating real mesh to delete the overlapping vertices - so it may slow down viewport performance slightly, and render times are slightly longer.