OK so I finally was able to finish the quest. Here are the steps I took, hope this helps others.
I left the planet, and came back. Went to the flophouse and started engaging all the scavengers. Worked my way all the way to the top to the far east building (You can turn off the alarms if you want). There is no marker for this on your map, once you approach the correct building SAM will talk about hacking the security. Inside the building there are 2 terminals, one of them you "hack" which starts a wave of enemies. Once complete the bottom building is unlocked and you can proceed with finishing the quest. As soon as the quest completed I got an updated quest to build the outpost. I believe the bug is that you can complete the Remnant core quest before engaging this side of the flophouse, which is what I did. That door should be locked until this is completed to prevent this from happening.
I followed this to make sure I was not missing anything. Hopefully this helps other out with this bug.
http://masseffectandromeda.wiki.fextralife.com/The+Flophouse
Very frustration EA, I spent 4 hours trying to figure this out with 100% viability on Elaaden. Please fix this quest.
Confirmed. Leaving planet coming back and FULL clearing (to find where you messed up) and SAM will set you straight.
