If you don't like the show because of the time issues (sure, there's lots of them, but so way, it's TV for God's sakes!!), then don't watch it.
Problem solved.
Their was only four people that knew jack was alive.Tony, michelle, palmer and chloe.How on earth would the russians know this or even frame him for their deaths.I don't think Chloe would have told spencer, thats just too easy. Now, on the otherhand, Derek, in his pursuit to find out who jack realy is to protect his mom, sends a fingerprint somehow to LE for identification. He gets nothing back from the cops but someone somewhere ( The Feds) has flagged anyone that searches for Jack's print.Now that the feds know jack is alive the ruskies somehow find out. Palmer was the primary target but he would have never blown his cover unles one of his friends was in Immediate danger.