We've encountered a persistent issue with colors within our submissions, specifically regarding those using Adobe Illustrator.
The prevalent cause for this is having the 'Color Mode' for the document set as CMYK instead of RGB. This converts all RGB colors to CMYK formats - including imported Color Guides!
CMYK Color Formats are usually used for Prints, whereas RGB Color Formats are used for Digital Images.
To change the Color Mode, go to:
File --> Document Color Mode --> RGB Color Mode.
Once you've done that, make sure to re-import the Color Guide(s) and apply the new colors for your Strokes and Fills. Don't forget to update the Swatches (if you've made them previously in the CMYK Mode).
Here is a comparison between the Color Modes:
(If you'll pay close attention, you'll notice that Twilight's coat color is duller in CMYK).
(Lyra has a more extreme change between the Color Modes).
So make sure you've set the Color Mode before working on your Vector and Importing Images to avoid any issues.
What's the difference?
CMYK colors are created with printed work in mind. Vector art is very useful for printing because of it's ability to be scaled infinitely, which is why Illustrator often uses CMYK color mode.
CMYK is more limited than RGB because CMYK is made from ink, whereas RGB is made from light. CMYK is made of cyan, magenta, yellow, and black ink, much like your printer at home probably uses. Printing presses use these same colors to make full color printed work. Though you can make a lot of colors with those four, it's difficult to get brighter colors like those used in most of the ponies.
RGB is what your computer uses to create colors. It creates images from red, green, and blue light. Most monitors and TVs work this way. RGB colors will often be much brighter than CMYK colors because they are less limited, and it is also what the show itself uses (because it's made for looking at on a TV). If you are creating vectors to be displayed on the web (such as say, here on dA), then you will want to use the less limited RGB spectrum.