Could not reproduce in 10.5.1. A couple of notes on the bug steps. I assume the intention is to include the relationships. If this is the case, then the relationship class must not be based on the OID column (I used globalids). Also, you must include the relationship table explicitly. In my case, I have the feature class, rel class and table in the service (layers 0,1,2). The LayerQueries should look something like this:
{
"0":{"where":"objectid_1 in (1,2)", "useGeometry": false, "includeRelated": true,
"queryOption": "useFilter"},
"1":{"includeRelated": true, "queryOption": "none"},
"2":{"includeRelated": true, "queryOption": "none"}
}