I'm running QGIS 2.6 on a Mac, and trying to create buffers around a point shapefile. The process seems to work: (Vector>Geoprocessing Tools> Buffer(s), I select my input layer, leave the segments at 5, and set the distance, create a new output shapefile in the same folder as the input layer, and set the new layer to appear.

A layer IS created, but it's an ovoid ellipse that is massively too large - when I set it for '500 metres', it came out covering most of Eurasia and Africa! I tested the settings, and to at '0.01 metres', it produced an ellipse measuring approx 1200x1450 metres.

What is causing this, and how do I fix it?

I wonder if it's related to the co-ordinate system I'm using, as the project is WGS84-PseudoMercator and the input shapefile is WGS84. I didn't intentionally make them different.