Duplicate tv shows containing different episodes

Hey. Strange issue that is effecting the majority of my tv shows. I use an emby server.

Under tv shows, I have multiple folders for the same show, in each folder there is multiple series, under the series there is different episodes.

See the attached photo or Alex Rider as an example.

But, if I make the Alex rider main folder a favourite, all the eps appear.

Hopefully this makes sense.