When configuring the default web server (uHTTPd) to use PHP you probably change the root www folder or other uHTTPd configuration. The LuCI web interface is a CGI web application thats runs over the same uHTTPd web server instance at port 80.
If was this, the best way do fix it is reset all the board pushing the "Reset WiFi button" (button near the USB connector) for more than 30 seconds - if you do this, the Arduino will be reset to all original factory configurations and software packages (ALERT: this procedure may be delete all local files). See Arduino Yun Getting Started to detailed instructions (https://www.arduino.cc/en/Guide/ArduinoYunLin)
Good luck 