The 'assembly' resource contains an array of Links (named "components[]") that reference the 'component' resources that make up that assembly. The 'component' resource as an attribute (named "operations_uri") that references an 'operations' resource that contains an array of Links (named "operation_links[]") that reference the 'operation' resources for that component. These two methods of indicating containment ("this assembly contains these components", "this component contains these operations") are inconsistent.
This inconsistency makes it harder to right clients for the API.

This is only one example of such an inconsistency. There may be others that should be processed in the context of this issue.