Mission taking longer than estimate

What is likely going on here is that the aircraft is getting slowed down due to lighting conditions to a value that is less than what the initial calculations were set for. For example, if you set it for 8 m/s and it determines that you are flying low with a low light level it might slow you down to 2 or 3 m/s and make it take much longer.

You can keep this from happening by disabling the "Slow Aircraft According to Flight Conditions" setting but you will risk flying too fast for the amount of available light. You will see that this is the case if the Ground Smear number is turning yellow or red on the Flight Stats panel.

http://support.dronesmadeeasy.com/hc/en-us/articles/208235483