Obviously, it looks like a very simple issue. The following 2D facet 1 can be plotted without error. However, the facet plot mixes up colors and shapes. For instance, in this example the right hand column typically should only have blue marker, while the center column should show green ones.
data1
num delay claim supply project
1 -236.347551 3000 DIF site1
2 65.132011 5000 Hoc site2
3 61.401260 5000 Hoc site2
..
base04 <- ggplot(data1, aes(num, delay, size=claim, color=supply, shape=project))
base04 + geom_point() + facet_grid( project ~ supply )
Any ideas from your side ..