Not exactly a death but....
Building a construction complex to make more microchips. Apparently I misplaced a station by a inch or something and it clipped into another station and I didn't notice.... the game, by the way, is perfectly happy to let you do this with absolutely no warning or indication whatsoever. Sitting in the sector taking care of my business, when suddenly the complex explodes, because the shields finally got worn down from the constant low collision damage.
Fortunately I have a save from before I placed the stations, but it was like 3 hours of gameplay ago and placing large numbers of stations is super tedious and frustrating so I'm considering just giving up and never doing that mission or cheating in the microchips I need.
X3: terran conflict. It's a decent game but man, the station building is so unforgivably terrible and you have to build hundreds of stations to get
the 75,000 required microchips for the hub mission.
Even ignoring the time spent getting the money, and ignoring the time spent by the factories actually producing the goods, you're looking at several hours just building stations using the worst station building UI ever and watching the same short, unskippable cutscene hundreds of times.