FULL PRODUCT VERSION :
java version "9.0.4"
Java(TM) SE Runtime Environment (build 9.0.4+11)
Java HotSpot(TM) 64-Bit Server VM (build 9.0.4+11, mixed mode)


ADDITIONAL OS VERSION INFORMATION :
Linux PROJ093 4.13.0-32-generic #35-Ubuntu SMP Thu Jan 25 09:13:46 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux


A DESCRIPTION OF THE PROBLEM :
Example URI string parsed by new URI(string) that contains an encoded reserved character "#" (%23) in the query string:

http://localhost:34455/ldp-test-43272e5c-1e3f-4bb8-8541-fa5ea6d6567a?predicate=http%3A%2F%2Fwww.w3.org%2Fns%2Foa%23hasBody

The URI object is then simply passed to HttpRequest.newBuilder(uri)

The server response shows this:
127.0.0.1 - - [22/Feb/2018:10:30:51 +0000] "GET /ldp-test-43272e5c-
1e3f-4bb8-8541-fa5ea6d6567a?predicate=http://www.w3.org/ns/oa
HTTP/1.1" 200 3 "-" "-" 64

Note that the encoded query param value for predicate seems to have been decoded and the string is truncated from the "#" to the end.

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
final String predicate = URLEncoder.encode("http://www.w3.org/ns/oa#hasBody", StandardCharsets.UTF_8.toString());
final URI uri = new URI(identifier + "?predicate=" + predicate);
final HttpRequest req = HttpRequest.newBuilder(uri).GET().build();
final HttpResponse<String> response = client.send(req, asString());

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
127.0.0.1 - - [22/Feb/2018:10:30:51 +0000] "GET /ldp-test-43272e5c-
1e3f-4bb8-8541-fa5ea6d6567a?predicate=http%3A%2F%2Fwww.w3.org%2Fns%2Foa%23hasBody
HTTP/1.1" 200 795 "-" "-" 64
ACTUAL -
127.0.0.1 - - [22/Feb/2018:10:30:51 +0000] "GET /ldp-test-43272e5c-
1e3f-4bb8-8541-fa5ea6d6567a?predicate=http://www.w3.org/ns/oa
HTTP/1.1" 200 3 "-" "-" 64

REPRODUCIBILITY :
This bug can be reproduced always.