This has happened twice in games now, and seems weird to me. I am playing with 3.14 patch I think.

Firstly can spies sabotage production of alraedy built space ship parts already added to the space ship as this must have happened 6-7 times in the game I finally finished last night. Also on at least one occasion the little red spy marker to show where the event had happened pointed to a city I hadn't even built a part in. I finally won but not until 2034 and after some frustration.

Is this a known bug and I need a newer patch or what...

It's a feature, there is a special mission to destroy (completed) SS parts. Personally, I think it should be available only in the capital or at least only in cities that built some parts, but that' not how it works. In any case, conducting a counterespionage mission helps greatly as it's rather expensive.