Paths not matching on map, while they do in Illustrator

I’m quite a newcomer when it comes to map data.

I have an Illustrator map, drawn by myself, with different polygons (regions, country, …).
In Illustrator I know 100% that the region and country line are perfectly in the same position.

I then used MAPublisher to export these to KML files, to then convert them into GeoJSON files.

I use these GeoJSON files together with Leaflet to generate polygons in the shape of what I have drawn in Illustrator.

But as you can see in the following picture, when I zoom in, the lines of regions and country are not in the same position.

Any ideas why this is the case?