Adding blocks to a ship as astronaut is fine, it adds structure HP and/or armor HP. When you remove blocks as astronaut it doesn't update it so your ship will have more HP than it has in terms of blocks. This can cause ship cores to be come invulnerable.
How to reproduce:
# spawn shipcore
# add a few blocks to it (as astronaut or in build mode, doesn't matter)
# remove them all as astronaut
# notice that your ship HP and armor HP is unchanged