Hello
If the reader worked prior to upgrading to 10.11.x, then you may need to update the drivers for the Reader to be compliant with the new OSX version.
Based on the model of reader you have, please look for a version which is compliant with 10.11.x
This thread describes how to rectify this issue, with a link to update drivers;
Additionally, you will need to be at the latest version of Centrify Express as well, in order to Support OSX 10.11.x
https://www.centrify.com/express/smart-card-form/
Once this is completed, and you are able to see the card reader light up when the card is connected, then you should next see the card details in the KeyChain. Because the light is not lighting when the card is connected, it generally means there is a problem with OSX and the reader itself.
I hope this helps! If not, please let us know the model of your reader as well as the version of Centrify you have installed.
Have a great day!
Ryan V