I was taught at school that diagrams in science are only ever done in pencil. They should be labelled with ruled lines and again in pencil.
Ds' teacher (year3) gives out extra stars ( their reward system) for neatly coloured in diagrams. For example last week's science hwk was to draw and label a diagram of a flowering plant, showing roots, leaves, stem and flowers. Ds did a neat pencil diagram just of the plant and labelled the bits. When we .got to school another child who had drawn a plant, coloured it and coloured the sky and grass was being complimented on the fantastic effort she had put into her work.
Obviously this is a very minor problem and I wouldn't dream of saying anything to the teacher but I am right aren't i?