Atmega32u4 on 5V. MISO from IC on 3.3V?
In datasheet ATMEGA328, Page 258,

Vhigh(min) = 0.6Vcc, considering Vcc=5V, then, Vigh = 3V.
Although MISO acting as input will work on 3.3V but you would be working on the edge. If the Vcc goes low, you would not be able to read a signal.
Recommendation: Try using a level-shifter(easy to build,3.3V to 5V) or optocoupler(different voltage references) for the same.