No, that fluctuation is normal, if you just see the line graph, sure seems to be a lot of voltage difference, but if you see the numbers, the voltage variation was just 0.06Volts, that must not be a problem to the PIX. One time I was runing a Pix with 4.2V (dont do it), and works, but the idea is not to work under 5V, so you VCC is normal.
What can make your pix reset is the current on the pix cant be delivered to all the electronics. Thats why I have asked you what do you have connected to the board. One time I have connected 2 TFMini distance sensor to my Pixhawk 2.1 Cube, and at the moment of the takeoff, the pix reset. Taking the TFMini power to the 5V BEC did the trick and no more reset.
Let me know about your electronics connected to your pix, bye!