Yes this bug has been around since SH3.
3 Simple rules for saving are :-
1. Never save if closer than 50Km from a port. As ships can loose there waypoints and crash (This was in SH3 but I still use. So I'm unsure if this still applies).
2. Never save if closer than 50Km to other ships (As damage and waypoints are not saved). As you just found out.
3. Never save while submerged (not sure if this still applies to SH5, but I still use this rule).
