In Inkscape every shape is colored the same, however when I view it in my browser all but one of the shapes is much darker. I viewed the file in other browsers and I get the same issue, so it's not just my browser. I've noticed this problem on other projects I've worked on as well. What seems to be the issue?

Check for any transparent color values perhaps.

As in the opacity slider?

Please check here:

Yep, all of the values are the same.

Mmh - can you put a white rectangle as a background behind everything and check if that makes any difference?

Just tried it and nope, no difference.

I run out of guesswork. Can you upload the file by any chance?

Sure. Thanks for the help!

I can´t find any discrepancies. I deleted the clipping path and put everything on a Layer1 instead of root. Please check out: I zipped the file, the original file has 124k nodes going on and 1,8MB in size won´t upload properly from here for whatever reason.

Thank you, I just checked it and I'm still getting the weird colors. I guess it's just on my end for whatever reason.

Bummer. 🤔

Reproduced here in Chrome but not FF. 

This is caused by the style color-interpolation:linearRGB

Agree. Search and replace with nothing resolves the issue.

NB: The document can be cleaned to remove hundreds of unused clip objects, and many of the paths include infinitesimally small loops and shapes that may cause issues down the line. If there are issues popping up regularly, I'd break apart the paths and remove internal loops, and generally simplify the paths. Map data is handy, but usually has more information than needed for infographic uses.

Thank you Tyler and Aero, it worked!