This issue only happens with downloaded seasons on iTunes. For instance, if 5 out of 10 shows in a particular season are available for download (the rest haven't aired), the first five will be grouped together in iTunes. Then, next week when show six airs it downloads into it's own grouping. Show seven gets its own, show eight, etc. If I download a season that has already aired so all shows are available for download, they all go into the same grouping.
All of the data on the show is on the same in all tabs except for the episode number, ID and description. The show and season information is the same (including spellings and punctuation).