I recently installed a hot water circulation pump and now get occasional whininf noise in the pipes, usually when flushing the toilets. There is also a expansion tank on the system and I have PEX supply lines.

If you get whistling noise only after toilet flush the chances are it is the toilet fill valve or angle stops that are making the noise. Noise is usually caused by partially closed angle stop or debris in fill valves. First, try to Close and Open angle stops for each toilet. See if that helps... If not, clean fill valves at each toilet...

Yes, hot water circulation pump can cause noise in your pipes. However, it is connected to the hot water side of your plumbing system therefore not really effecting cold water side and toilets. So in this situation the chances are small that the noise is being generated by the pump.