I have a multisite with 8 different languages.
One of them is Estonian, which has the locale "et".
However, the country code for Estonia is actually "ee".
(The full locale for estonia is et_EE)
The correct language flag for estonian would be ee.png, but currently it is showing the Ethiopian flag et.png
I imagine there could be more cases like this for other countries/languages, so I guess the easiest solution would be to create some exceptions in the plugin code to handle these cases.
Another possible solution would be if there was a way to configure the flag code per site. So if I was looking at the configuration on the estonian site, there could be a field for language code and I could insert the language code manually.