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I have just ripped disc 1 of BTCAS and it appears some content is missing. I have all the episodes and special features, but the first 5 episodes are supposed to have a short introduction from the creator Bruce Timm talking about the episode. However the ripped content has only 2 of these introductions and they aren't even in order (e.g. first 2) it's episode 3 and 5 that only have the Bruce Timm introductions. Does anyone know what could be the problem?

It is possible the introductions are shorter than the default minimum title length of 120 seconds. MakeMKV skips titles that are shorter than whatever the minimum title length is set to. Lower that value and try again.

The "Episode with introduction" might be a menu "thing", or it might be a separate play list.