After Series One, Howard and especially Vince undergo Flanderisation. Vince becomes far more obsessed with fame and partying and becomes a lot more shallow and cruel. At first it looks like standard flanderisation, but in "Strange Tale Of The Crack Fox", it was revealed the Crack Fox used to be a friendly fox until he moved to London and became an evil drug addict, because the London Lifestyle is incredibly corrupting. In Series One, Vince and Howard lived in London, but they spent most of their free time at the zoo and although Vince had a social life, neither were really involved in the London night life. When they moved into a flat in Series Two they were put right in the heart of London, and the London Lifestyle corrupted Vince (And Howard to a smaller degree) just like it did the Crack Fox.
In The Hitcher's third appearance, he appears to have lost his haggard skin and witch-like nose. At first, it may appear to be laziness or forgetfulness on the wardrobe department's behalf... then you remember that you last saw him being melted in the Fountain of Youth.
In "Eels", at the shaman stag weekend, why is Tony Harrison the most drunk out of all of them? He has the smallest body weight, meaning that his alcohol tolerance is lower than the rest of them.
The Retools each season might seem like loose continuity, but they actually make sense if you think about it. The Zooniverse likely closed at the end of series 1. After Dixon Bainbridge disappeared in "Charlie", there was nothing stopping the lawyers from "Jungle" from taking over, and all the maulings in "Hitcher" were probably the last straw for the zoo. After losing their jobs at the end of series 1, Howard and Vince decide to focus on their music career (an interest hinted at in "Electro" and "Hitcher") and need somewhere to live, so they move in with Naboo. Throughout Series 2, they repeatedly screw up their chances at going anywhere career-wise with their music (culminating in when they miss the Pie Face Showcase in "Milky Joe"), so they need to get day jobs. Thus they start working for Naboo. This is supported by the fact that Bob Fossil also has a new job as of series 3.