This came from a GO helpdesk query, but would probably be generally useful:
Can a verification check be created that would detect when one term has two (or more) synonyms with the same text string? If the scope, category or dxref differ, the identical synonyms should still be reported, because a given synonym should only have one scope, and multiple categories or xrefs can be included in one line in the file.
relevant tags from two examples in GO (e.g. http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/~checkout~/go/ontology/editors/gene_ontology_write.obo?rev=1.1766;content-type=text%2Fplain - fixed in later revisions)