As /u/cfj@feddit.uk said, make sure they’re in separate folders. It should be something like \TV\show\season. If you have nested folders this can really mess it up, for example all the seasons might be combined into one.

Aside from that, if you go into the Dashboard and then metadata you can manually edit everything. However I don’t think this will let you split apart two shows that are stuck together after being read from the same folder.