2012 13" Macbook Pro (nominal 2.5 Ghz) runs constantly at 2.9 Ghz
The Late-2012 13" MacBook Pro Retina comes in two variants - one is a 2.5 Ghz i5 CPU, and the other is a 2.9 Ghz i7 CPU. 

If you have the 2.9 Ghz i7 variant, then this is why your machine is running at 2.9 Ghz.

The 2.5 Ghz i5 CPU supports TurboBoost which allows the CPU to boost its frequency from 2.5 Ghz up to a maximum of 3.1 Ghz. In simple terms, the boost is effective only when one of the two cores are busy, but the other is not. This occurs for example when you're really only running one, single-threaded application program.