I do see this occur at times. From what I can gather it only happens when the game decides to spawn the vehicle inches off of the ground, and then when you get in it, it falls a very short distance. The vehicle takes insane amounts of damage for whatever reason, and then boom.
Placing base parts in a heli has always been iffy since when you release it, the base part becomes a collideable object for a second. If the heli is spooled up, it will destroy it and even if it's turned off it can occur. I would always use the Load In Vehicle option or if you look at the heli from an extreme angle (Standing next to the cockpit but looking far past it's nose) it usually works out all right.