Late reply, but others may also encounter this. To the best of my knowledge, yes, sometimes the ship just blows up long before you have any chance to get to it. It sucks, but you just have to try again. I had the same issue in my last play through (with the original game discs) and I seem to recall reading others complaining about it online.

There's another buggy mission where you have to meet some guy inside air vents for a key. The mission objective doesn't tell you where he is, and if you continue down the vents, you can't get back up. You must go down a floor through the grates where there is fans, use the map to see where the guy is hiding. You may have to shoot a vent cover to get access.

This map is also riddled with multiple secret shortcuts. There are destructible white doors, be careful or do not open them. One leads to a blue tunnel straight down to the locked door, another leads to a higher exit point at the locked door.

If you have too much trouble, you can use the glider cheat (hit escape type buzz), which if you use in an enclosed space like a vent, glitches you up backwards.