So this weird thing happened to me he other day. I left a space station after about an hour or so of trading, and started flying towards a new planet in the system I've been hanging out in. As I started activating my pulse drive, there were notifications of hostile ships in the area, or approaching. I thought, "good riddance" as I made my way towards my destination. But then the space battle music started up, and my ship's pulse drive deactivated. One pirate was in the area, and I shot it down, but the music kept on, and the screen said there was still one more pirate. The problem was, when I maneuvered around to face it, there was nothing inside the crosshairs but the space station I had left, noting a 1 hour travel time (since I had pulsed out already).
It seems like what happened was that the pirate sequence triggered as I was leaving that area, and the game didn't register the fact that I was in the clear. I faced back towards the planet I was flying to, but it was hours away too. I couldn't activate my pulse drive either, because the game still thought I was near the pirates. After about five minutes of flying back towards the space station, I turned off the game. I wasn't about to sit around with my thumb on the circle button for an hour, so I figured I'd reload the game and start back from the last save point.
Then I reloaded, and realized the last save was back on the space station, BEFORE I had made any of my trades. It's not enough to ruin the experience, but still a frustrating loss of time.