How to wire the two AVcc pins on ATmega32u4 when only using some ADC pins
Both of these groups of pins have a nearby AVcc pin, which is used to
  power the analog part of the micro, and as a voltage reference for the
  ADC


Both need to be connected to Vcc via a filter for best performance. See this note on page 307: -


  Note: The same circuitry should be used for AVCC filtering on the
  ADC8-ADC13 side