Yeah it happens...I took a Wing job to move a few thousand widgets from port A to port B in a system. First 3 trips were uneventful. The 4th trip, a pirate shows up. I break interdiction, thought, "Well, that was that". Nope. Same pirate, different ship, was waiting for me when I launched. This mission took 22 back and forth trips (44 total) at this point. Guess who was waiting at each launch.
As it was an almost 11 Million payout, and the Penalty for failure was just over 50 MILLION...and I only had 53 million in the bank, I figured my interdiction avoidance skills were better than the NPC's ability to interdict me. Finished the mission, got my money, never saw Pirate Dude again.
So, yeah, it can happen...it's a big galaxy.
Take Care and Check Six Commanders! o7