Não. O comportamento descrito é normal.
Também fiz uma pergunta semelhante sobre o Crunchyroll ( CR), onde a ocorrência é mais prevalente. Um membro chamado beardfist (que desenvolveu um player HTML5 para CR) foi um dos respondedores:
The problems you are describing are a symptom of the auto-play (or perhaps more accurately auto-advance) implementation that CR (and YT to some extent) use. Basically for anime while you are full screen, if you allow it to advance to the next episode it will load the next stream all nice and neat without making you hit full screen again (this is relatively new for CR).. When that happens, the rest of the page hasn't been changed at all, so when you come out of full screen, it loads the correct page for that episode. Since the only part of the episode page that is modular is the comment section, with the rest being sent as a big chunk, it really is the easiest way to do it, even if it isn't the best experience.
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While it is possible to implement the video player and manga viewer in such a way that this refresh doesn't happen, doing so in the current flash versions would not be worth the time it would take, imo. There are HTML5 versions of both that are in various stages of in the works and while that may be something on the todo list, most likely they will opt to still have the page refresh when you come out of full screen just as youtube does.
Vou informá-lo sobre esta questão do SE para que ele conheça essa citação extensa e tenha a oportunidade de comentar se assim desejar.