Background
For an explanation of what indexed color spaces are, read the following knowledge base article.

Solution
PDF/X-1a and PDF/X-3 both allow indexed color spaces as long as the base space is an allowed color space in the particular PDF/X standard used.
For example, if the file is a PDF/X-1a file, the base space of any indexed color spaces must be either gray, CMYK or a correct spot color.