45 mins is a long delay due to not being able to get a flight plan out of the system but maybe the crew simplified!
Maybe there was a 10/15 min delay in getting the paperwork due to I.T issues (we all have them!). Therefore they missed a slot or the ground crew had to dispatch another aircraft first delaying your aircrafts departure.
Arriving late into Pisa means that instead of being number 1 you are now number 5 on approach and therefore slowed down really early adding another 5 mins on to the flight time. A small delay soon snowballs into a bigger one through no fault of your own!
I am sure the crew were being honest and there was no sinister cover up going on!