Yes, and I do think it's meant to caricaturize real problems in our own society; yes, our criminal justice system isn't so broken as to flatly deny the right of trial when it sees fit, nor is our government so inefficient as to enable teenagers to regularly break into parts of it that would be akin to the FBI/CIA (Department of Mysteries), but they do reflect legitimate themes of injustice and problems with bureaucracy that resonate in the real world. And I say "our," but I suspect her main focus was likely the British government, yet these do seem to be universal problems.
I think also we sometimes forget these books are meant for children, so it all needs to be exaggerated to bring the point home to a 10 year old. Studies have been done which conclude that children who read the Harry Potter series grew up to be less prejudiced than peers who didn't, so there must be some merit to it all.