Pulling this thread back on topic, I've heard a lot of lamenting over the idea that Neelix's jealousy of Tom kept cropping up and had started to 'get old' by the time Partuition came along, but I really don't understand that line of thinking. Jealousy is an emotional flaw, and unless it's addressed, it's not just suddenly going to go away. Neelix insisted he was over being jealous of Tom spending time with Kes, but he hadn't actually addressed the root of the problem, which is entirely understandable, and the fact that it continued to surface is actually a good thing when it comes to characterization continuity, even if it's not an aspect of Neelix's characterization that is particularly flattering.
Another little piece of continuity I noticed - and that would've been more effective if episodes had been aired in production order - is Harry owning/playing the clarinet, which is set up as a matter of background 'noise' in Non-Sequitur and then used as a focal point of the scene in Partuition where Tom admits to Harry that he's falling in love/has fallen in love with Kes.
I've spent much of this thread talking about instances in which the show demonstrates continuity positively, but, since I've already acknowledged that it wasn't perfect when it came to balancing the issues of episodic storytelling, serialized storytelling, and story continuity, I figure it's time to mention some of the things that are clearly inconsistencies, starting with Walter Baxter's changing uniform. When he's first introduced in Eye of the Needle, he's wearing a red Command Division uniform, but when he reappears in Twisted, he's wearing Operations Division gold and is serving in Security.
There's also the costuming inconsistency with regards to Tuvok's rank that persists from Caretaker through Cathexis, and the costuming 'downgrading' of Tom from a full Lieutenant to a Lt. Jr. Grade that also happens in Cathexis.
I don't personally think the Paris and Tuvok costuming inconsistenciess are that big a deal because they don't really affect things story-wise, but am
bugged ever so slightly by the Baxter one because his being a Security officer is directly addressed in Twisted when he encounters Tuvok and they talk about him (Baxter) needing to get back to his duty station, and it therefore would've been nice to have had his position as a Security officer established in his first appearance earlier in Season 1.