So, I’ve completed every zone 100%, but my planet progress says like 98%/99% for every planet. Is this a bug? or are there secret challenges I don’t know about?
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I think it may be a bug, I ran into the same issue on Pandora. Every location is 100% complete; however, the planet progression shows 98% because I’m apparently missing a location and mission.
Hopefully they fix this soon.
I have those and a related progress bug in the first zone where you can find a scrapped claptrap. It shows my progress as 0% but the icon for the location is check marked and grayed out.
I assumed it was because of the Eridian writing on each planet that you can’t read until later in the game.
My galaxy progress for eridian writing marks 35/30 even though i believe there is only 32.
i have meridian outskirts at 101% zone completion, very optimized game we waited 7 years for 
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update: got the achievement for the Eridian writing. It is now marked at 40/30 collected. If you collected all Eridian writings and still did not receive the achievement, just to to Sanctuary and spam the interact button on the Eridian writing (in the same room as Tannis) and it should give you the achievement.
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Did your zone progress update though? My Pandora is stuck with the same progress that you mentioned.
Did you find the slaughter shaft in Konrad’s hold?
Did today, and that was it. Thanks. Weird that the tracking showed 100% for the zones though.
Mine is also stuck. It shows 100% on everything and still says I need 2 locations and 2 side missions
The Drought: 101% complete…
So is this then a UI bug or maybe… something… dunno? 
I have some areas on 104% whats all that rubbish about.
I see 114% complete when I look at the big overview of everywhere I can go
Broken game is broken.
I have gotten the achievement but the % number is not correct. It is usually above 100%.