Content alignment issue

I’ve encountered a problem which I can’t fix. When there is a small amount of content on a page, it moves up the page and overlaps the menu bar. Here is an example.

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The problem resolves if there is content across the whole page. Here is an example of that:

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Same thing happens for the 404 page.

I really cant work out how to fix this so any help would be appreciated.

Many thanks.