We have an automated test which runs through all XML catalogs checking for broken referenced resources. It ran over the DITA OT 3.5.1 bundled XML catalog and reported these problems:
plugins/org.oasis-open.dita.techcomm.v2_0/dtd/bookmap/dtd/bookmap.ent does not exist referenced from plugins/org.oasis-open.dita.techcomm.v2_0/dtd/bookmap/catalog.xml
plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/dtd/concept.ent does not exist from plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/catalog.xml
plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/dtd/glossentry.ent does not exist referenced from plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/catalog.xml
plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/dtd/glossgroup.ent does not exist referenced from plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/catalog.xml
plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/dtd/reference.ent does not exist referenced from plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/catalog.xml
plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/dtd/task.ent does not exist referenced from plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/catalog.xml
plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/dtd/troubleshooting.ent does not exist referenced from plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/catalog.xml
plugins/org.oasis-open.dita.v2_0/dtd/subjectScheme/subjectScheme.ent does not exist referenced from plugins/org.oasis-open.dita.v2_0/dtd/subjectScheme/catalog.xml
plugins/org.oasis-open.dita.techcomm.v2_0/dtd/bookmap/dtd/bookmap.ent does not exist referenced from plugins/org.oasis-open.dita.techcomm.v2_0/dtd/bookmap/catalog.xml
plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/dtd/concept.ent does not exist referenced from plugins/org.oasis-open.dita.techcomm.v2_0/dtd/technicalContent/catalog.xml