Vectors do not necessarily need outlines- the one with outlines I guess you can call line art, the ones without the
outlines are called cell shaded.
If you're using Adobe Illustrator, I'm sure there's an option to turn the outlines off or at least to
0px. The swatches should be the same.
I guess you're trying to figure out the consistency of the outlined and lined scan- if you want to keep the
outlines, make them all the one colour (black, for example), or at least a darker tone to the one being coloured in
(cream face, brown outline).
Or just pretend they don't have outlines at all- it's up to you.