Any scenario where the SVG's shapes are rendered with anti-aliasing, and the edges of both overlapping shapes are mid-pixel: the edge of the top shape would be rendered with partial alpha, and then beneath that, the edge of the differently-colored lower shape would bleed through as it is also rendered, at that contiguous line, with partial alpha.

EDIT: You can actually see this very effect in action if you zoom in on the diagonal edges of the yellow and blue faces of the logo on the BBC's page for the EU referendum happening right now: http://www.bbc.com/news/politics/eu_referendum/results - on these anti-aliased diagonal edges (enlarged: http://i.imgur.com/GmxUD60.png), since there's no indentation like the one this SE question highlights, the red shape underneath both of the shapes bleeds through.

Compare the outlines of the shapes with the red shape conterminous beneath them (http://i.imgur.com/Nwyl8YE.png) to the outlines they have when that shape is removed (http://i.imgur.com/iOQmyJx.png).