Oh yeah, I know all about the filming xD once I started watching the show I went on the research page, and also read about the film crew/process of making the series and all. There weren't multiple Flowers, or Zaphods, though.
Ones that would be substituted sometimes were more 'background meerkats', like Mitch. The actual Mitch went missing (he left the reserve), but they just kept saying he was around and pointing out "Mitch the Super Sentry!!", long after he was gone. (A meerkat called Logan played him a lot of them time, as in they filmed Logan and would just call him Mitch on the show) Sophie was also sometimes played by a different meerkat, iirc. Their life isn't usually half as exciting as on the show P: And a few others. And a lot of the Meerkats have different names on the show than what they were actually called by the research team, because the producers said so. (Maybelline was actually called Monkulus)
Edit: Oh! and enemy mobs. They would often use footage from more than one encounter for a single encounter on the show, or repeat use.
On a happy note, look at Fluffernutter!
He's just so adorable xD never appeared on the show. He was born without claws/fangs, but managed to reach adulthood!