orConditionGroup() - unexpected result
I can't see any issues with your code, and this might be a dumb answer, but a while back I was having trouble with chaining together entity query conditions. I got everything working by splitting it into individual statements. It didn't seem logical that that should make a difference, but it did. (Though, I'm sure it's possible I had some other logical problem that was the actual issue, and separating into statements was just incidental.) But maybe try...

$group = $query-&gt;orConditionGroup();
$group-&gt;condition('field_ref1_user.entity:user.uid', $user-&gt;id());
$group-&gt;condition('field_ref2_user.entity:user.uid', $user-&gt;id());

$query-&gt;condition('status', 1);
$query-&gt;condition('type', 'mynodetype');
$query-&gt;condition($group);         
$ids = $query-&gt;execute();