I disagree that there is a discrepancy between the plots. Looking at the s1 facet plot, at an x value of 0.5, where there is a grid line, there is a small bar that represents about 100 counts. That is the small s1 feature that appears on your first, stacked, plot. Perhaps you are being confused by the stacked layout of the bars. Once the s1 and s2 bars overlap, the s1 bars are drawn on top of the s2 bars. You can see this in the bin that is just below the bin at 0.5. In the facet plot, s1 has about 200 counts at that value. In the stacked plot, the s1 bar is the same size but it is displayed with its base at about 400 counts and its top near 600 counts. You might think that there is more to the bar hidden behind the s2 bar but that is not true.
now the picture is clear to me , i always get confused with these parts .
facet will show you the grap similarly like position=identity and will not shift the overlapped parts to the top of the bars .