I also have the same issue... I already decrypted the shard, scanned everything around, the guy that was still alive when I arrived to the mission area is missing but I also scanned him the first time. Johnny is just sitting by the last body (close to the wall) without saying anything.
there is a point to scan below the trash on the left side of the area most people miss... its super stupid placed indeed - had problems to find that one as well the first time... since than i never had any problems to trigger that one on my 4 following chars...
the only bug i obtain on this quest is after defeating it the mystery horror sound stays 4ever.... no matter how far i leave the area - i need to reload to get rid of it... but lately i used it for rpg: let i played while was hunting target gigs at night - was pretty cool to sneak in buildings with my melee build and this sounds in the background xD
If you did not TALK to the dying guy mission get bugged and you would need to start from scratch.
There is a few ways this can happen.
You enter area and start scanning stuff, guy dies now it can never be completed.
Maybe you went to area but didn't want to do the mission at that time, again guy will die and now mission is bugged.
This might not even be a bug, it might be by design but they forget to fail the mission if you do not talk to the dying guy.
I'm also pretty sure you NEED to talk to dying guy BEFORE scanning or it will also bug out.
I know it's very hard but just really never ever SCAN anything unless stated in mission objectives because it is such a bad game design that if an object is scanned it can't be scanned again for mission updates, this is by far the most idiotic design in any game I ever played before. How this is not fixed even in patch 1.2 can only mean that the code behind is made in such a stupid way it might need a complete rewrite to work as it should have from release.