Unsure how relevant this may be to the OP's problem, but in the recent past I have had a CTD when loading a saved game, and on another saved game the sonar-plotted targets were missing on the surface... Deleting the saved games and starting a new career solved those problems. Annoying but not catastrophic. (Win 10 64 PC, 32GB RAM with NVidia graphics).
Likely an unrelated coincidence, but a bigger problem arose when my PC would freeze and become non responsive at varying intervals from a minute or two to more than an hour.
After using Safe Mode to confirm the bare bones of the PC were working normally, researching the "Windows freeze and not responding" problem led me to clearing the Windows File Explorer history following the instructions at
this website
For good measure I also cleared the SH4 saved games and started a new career. The computer has been glitch free for more than a day, SH4 plays flawlessly, and seems to have less stutter at higher TCs...