There could be various reasons of that. Starting from wrong configuration in bundle.xml to the wrong definition in compliance.data, or other input data files. In many cases pre.xml, and mat.xml files are created manually by customers, so there is a huge chance that there is some typo between provided data in .data files and mat/pre.xml files.
Many times customers creating custom specification by coping one of the out of the box compliance regulation and modyfing its content. This is good approach but you can forget to modify not only input.data files but also all XML files, and template.mf
I would check:
1) compliance data, if all information are correct, like numbers of columns (pipes), If categories in compliance data are pointing to the good regulation name and revision
like
|2|AZO DYES||30|Controlled|<=|1|2002|SPEC_NAME|SPEC_DATE_OCT_2013|2014-05-08|SPEC||||||||
2) check other input data files
Note* everywhere substances, regulation names, categories etc.. should be written in UPPERCASE.
3) Check mat.xml and pre.xml file. If you dont not use any tool (scripts) to generate those files then in 90% here could be an issue, due to missmatch data between XMLs and compliance data files
4)check bundle.xml
