The largest nation on Madagascar has zoomable borders and default border colour, unlike the rest. I assume this is not intentional. Also Comoros stays yellow and is behind the circles. Not sure if you wanted it that way. You could add a class to the circles and the island contours called "comoros" or something, use that as path ID for the nation on comoros and give the paths some other name. That is of course if the current situation is a makeshift solution to this problem and not actually intended.
Not intentional, but it mostly has to do with the fact that this is an older SVG when I wasn't aware of these solutions. I should probably fix it at one point lol.