Modern autofocus systems use mirrors that act as beam-splitters: most of the light is reflected to the viewfinder for metering and viewing, while the rest (typically 25%) is transmitted and then reflected by a secondary mirror to the autofocus sensor, which is in the camera body. With a polarizing filter attached, the ratio of reflected/transmitted light (fixed for non-polarized light) varies with the polarization plane orientation of polarized light, relative to the beam-splitter, causing the amount of light reaching the autofocus sensor to vary. This effect can be particularly troublesome if your front element moves with the lens, as it would cause the amount of light reaching the sensor to change while the lens focuses.
While you can see (rather easily) when your autofocus system has been confused by a linear polarizer, there isn't such an easy way of knowing whether or not the internal light metering system has been stumped.