When using colored pencil for Manga drawing, its easy to pick up tiny specks of color from dark areas, making streaks or spots through your lighter areas. To avoid this, work from light-to-dark, doing highlights and pale skin tones first, then adding darker shades and shadows last. Use a soft brush to flick away loose particles of colored pencil.
Use the same approach when using felt pen for coloring manga, and make sure that previous layers are dry before starting on a new color, if you need to avoid blending.
Pencil lines can often be a problem, with graphite pencil smudging into colors. Use a fairly hard pencil, and draw as lightly as possible, lifting off excess graphite with an eraser. Re-do linework after you've colored the drawing. Some artists like to use a smudgeproof Indian ink to ink drawings prior to coloring.