It looks like they’re loading the same library as us to have more advanced select boxes. However, their selector isn’t specific to their options, so their version is overriding our version, causing a conflict.
It doesn’t actually look like they even use it in the Customizer, so the best thing they can do is prevent select2 (the library) from initiating inside the Customizer.
Might be worth opening up a support ticket with them – if they need more info or have any questions just let me know.