From json-ld/json-ld.org#119 for examples and background:

The current behaviour avoids embedding the same data multiple times in the result makes it difficult to work with the output. A proposal to change this to "agressive re-embedding" is currently being discussed.

Using my own words:
Declaring "@embed" : "true" in the frame I would expect that object URIs would be embedded in all fields declared as such. But they are only once embedded (arbitrarily in one of the declared fields) - if the reference URI appears in different fields at the same time the other fields only get the reference URI, nothing is embedded there.

There are solutions in different languages, but not in java yet. Would be glad to have it here, too!

See also digitalbazaar/jsonld.js#20.
See also json-ld/json-ld.org#377.