In general, questions like these are much better asked in the Issues queue for the relevant module: http://drupal.org/project/issues/relation - you're more likely to find people who use the module and have encountered similar issues/know how to handle it. Be prepared to provide more details (e.g. what version you are using; when you say the module failed, what exactly happened; if you using similar modules like EntityReference etc)

I tried using Relation module to associate Taxonomy terms and the module failed. It relates some taxonomy terms but not others, I do not know what the differences may be that cause this discrepancy.

Now I get error message: Undefined index: relation in field_info_instances() (line 687 of /home/mydir/public_html/site/modules/field/field.info.inc I do not understand this error or how to fix it.