2.8V to 5V conversion not working as it should. Why?
A VL6180 board must have a stable 2.8V power supply (locally, at least the Sparkfun board has it), otherwise the sensor will have goofy unstable results. You need to use this rail to feed the low side of your interrupt level shifter instead of weak voltage divider. 

Or you can try a diode in series to drop the VL_IN voltage from 3.3 into 2.6-3.0 area instead of resistive divider (replace your 100k with a 1N4148 diode). 

And you will need a pull-up to 5V on the high-side of level shifter.

ADDITION: per suggestion of brhans, the min input level for ATMEGA32U4 is 0.2Vcc+0.9V = 1.9V, while even a fully loaded (8 mA) interrupt output from VL6180 should produce 2.4V, so no need in the level translator at all.