Fixed it? Was it broken? I could see them adding more cues to actions we take but luckily there is auto save for such things. I have lost a titan that way, not realizing it was caught in a 3 way fight by itself but that was 100% my fault for not paying attention.

Yes, I do consider it broken when I can accidently press a single key and blow up any of my ships and planets, or in other contexts end my turn. Making it require multiple keys fixes that problem for me.

I can also think of a few contexts where the existence of an auto-save function is not a sufficient solution, so coming up with other ideas feels appropriate.

Ships under attack (and valuable ships like capitals and titans) already have good, attention grabbing, alerts in place. An audio acknowledgment for scuttling could serve as "a more obvious alert." Or it might just be annoying. Red flashy text somewhere? Blocking the function for home planets or last remaining planet? Something that I haven't though up?

Or maybe you're right and the problem was just me, no further thoughts need be applied to the non-situation.

It's not broken. Don't accidentally push a key.
Better option for you would be to change the keybind to something less likely to be pushed unless specifically wanted. I have mine bound to shift+s.

Binding shift to hotkeys doesn't work as intended I believe. Shift is hardcoded to queue, so binding something to shift key combination will queue the action after the current order. Use with caution.

You are correct. Not sure if it is hard coded. Speaking to a dev they said that i should rebind it to something that isnt shift. SO probably so. 
Shift+s for scuttle isn't effected like using shift+r for retreat.

Thank you bringing this up, I can definitely see how this could be disruptive to the player experience, especially to new players, ill add it to my report to suggest to the team