Not all the fragments were collected or able to be reunited (which is why Prowl had to sacrifice himself). Presumably, Starscream was killed because he flew within range. The other clones (as well as Wreck-Gar and the Constructicons) are unknown as to whether they are alive or dead, but presumably they may still be alive. Two clones are definitely still alive (Sunstorm and Ramjet) as they were on Cybertron and Prowl was only able to gather fragments from around the city area.