I've read a couple reports that if the suspect is "aggressive" and "represents a threat to the officers safety" they are not held to the seat belt policy. I'll see if I can find the article.
EDIT:
Freddie Gray death Baltimore police prisoner transport under scrutiny - World - CBC News
This is not one of the articles I'd originally read, but it appears it might support the angle the other article I read was going for. The policy states "seat belts or other authorized restraining devices." Also says that the other prisoner in the van told them Gray was moving around, kicking, and making noises up until the van arrived at the station, and also that the driver was not giving them a rough ride. Maybe something happened when they unloaded him?
"It is police policy that all arrestees must be buckled in during transport. The policy, updated just nine days before Freddie Gray was injured, states "all passengers, regardless of age and location, shall be restrained by seat belts
or other authorized restraining devices."
An attorney representing one of the six officers involved in Gray's arrest said it can sometimes be difficult, or even dangerous, for officers to belt prisoners if they're agitated.
"It is not always possible or safe for officers to enter the rear of those transport vans that are very small, and this one was very small."
[...]
"Batts said another man who was in the van during the tail end of Gray's ride told investigators that Gray was "
was still moving around, that he was kicking and making noises" up until the van arrived at the station. Batts said the man also said the driver did not speed, make sudden stops of "drive erratically."
But Batts was careful to say that the investigation includes "everything the officers did that day."