Look at the 2nd and 3rd flights which are at irregular times.

GIG-LIS Mon 7/10 5:40p-7:20a
LIS-GIG Tue 7/11 11:35a-5:35p
GIG-LIS Tue 7/11 7:50p-9:30a
LIS-GIG Wed 7/12 10:05a-4:10p

It occured to me that Portugal had to finish the UEFA soccer game against France (and won!), and after a restful night's sleep, maybe the time needed for them to pack was projected to delay the flight to the olympics in Rio two hours. Do you think this makes sense?

Added 7/12: the reason the Tue LIS-GIG was scheduled for two hours later was per a flight attendant that their requirements are twelve hours of break time, and various factors made it a bit tight prior to the flight.