I've noticed that there was a little movement at the base when I wiggled the end of the aerial.

When it's rained and I do it, some water bubbles out so there's clearly water getting under the base. As it was reasoning again yesterday, I stopped by a Skoda dealer I happened to be passing and whilst the fins on their Yeti didn't have quite as much movement as mine, they were still squeezing out liquid when I moved the rod.

I'm surprised that there's water getting over there, but as it's not just mine would I be right not to worry?

Remembering the back door seals on my Fabia, knowing it's not just my Yeti isn't that reassuring...

Given that the Yeti has been around for 5 years and nobody has reported a problem, I don't think you need to worry.