Were you in "Supergroup Mode" when you hit all the locations?
Unexplained Investigations Supergroup on VICTORY!
UI Cards
Snuph's Hero Helpers
Well, assuming you were in SG mode the whole time, I would think you missed one because the server was laggy. When getting an exploration badge for the first time (so I get a notification), I've seen it take close to 10 seconds to tell me I got the badge.
So, when I'm re-getting a badge I already have for SG credit, I make sure to stand right on top of the marker for 10 seconds or so.
Paragon City Search And Rescue
The Mentor Project
Also make sure you have ALL the badges you can get.
I17 in particular added new explore badges to the game.
You can always check with what's listed on sites like Paragonwiki.
Good Luck. 
Loth 50 Fire/Rad Controller [1392 Badges] [300 non-AE Souvenirs]
Ryver 50 Ele� Blaster [1392 Badges]
Silandra 50 Peacebringer [1138 Badges] [No Redside Badges]
--{=====> Virtue ♀
Thank you for your fast response. Yes I am in SG mode and i just looked up i17 new badges and tried that and still didnt get the SG credit. I will check a few more sites to see if I am missing something if not I guess I will ticket it.
All city zones now have an accolade associated with them now as well, so you could check the accolade page to see how many in a given zone did not register. Doesn't help you find the ones you are missing, but could be helpful.
Liberty Server (@enderbean)
Arcs on Live
#1460 Hometown Rivalry
Just started playing after about a year of vacation. moved one of my toons to another server and started a SG. Went exploring for badges and got them all but when i finished Nerva Archipelago and Grandville my SG did'nt get credit for it. Anyone know what I did wrong?