The edges in places might look a little ragged when zoomed, but I don't see any partial grid lines or stray marks (Mathematica 11.0.0.0 on macOS 10.11.6).
Export["uglypiechart.pdf",
PieChart3D[{9.69, 25.49, 21.36, 9.69, 1.80, 31.96},
ChartLegends -> {{"grade > A 9.7%", "A > grade > B 25.4%",
"B > grade > C 21.4%", "C > grade > D 9.7%",
"D > grade > E 1.8%", "no grade 32%"}},
ChartStyle -> {"CandyColors"},
ChartLabels -> {"9.7", "25.4", "21.4", "9.7", "1.8", "32"}]]
Attachments:
