When looking very closely at my shapes, the fill is not following the paths I have defined. I have attached a screen shot where you see the blue does not go all the way to the red path. I have never seen this issue before.
If it steers anyone in the right direction, I can replicate it, having experienced it in the past. I can't remember if I managed to fix it.
For me, this only happens when creating a 72ppi RGB document, and then upscaling it (Effect > Document raster effects settings...) to 300ppi. For now, I can only view this at 17,000% zoom: https://postimg.org/image/w797ceuw3/
What % zoom do you have set to get this result, Jessica? If you can, it may be worth pasting everything in to a new, 300ppi document.
I know this question is 4 years old, but I thought I'd share an answer I discovered on the Adobe forum thread here: (https://community.adobe.com/t5/illustrator/fill-doesn-t-match-the-path-created/td-p/10474435)
The solution is: View > View using CPU
For whatever reason, the GPU view was messing with some of my anchor points, extending the fill color out in an odd, squared-off way beyond the path (image 1 below). I switched it to CPU, and it cleared right up (image 2 below). Hope this helps anyone else coming here for an answer to this question!