Note: this was done in Classic, but as the bug also exists in Remastered, this might help for that, as well.
People have been running into a problem in HW1R where all the objectives get completed in SuperNova Station, but the level doesn’t finish. It just sits there.
The problem isn’t in the Remastering, I don’t think. I believe it’s in the original game. I just completed the level in Classic. All the enemy ships are destroyed, but the objective to destroy them refuses to be marked as complete.
The only difference between Remastered and Classic with this bug is whether or not the objective indicates as finished. The result is the same: the level never ends, so it needs to be restarted from the beginning.
EDIT: Ok, I think I figured out what’s going on. Upon attacking the station, one of my Ion Frigates decided to leave. I went out into sensors manager, and discovered that one of my ships was flying off into nowhereland (seriously; if the station is north and the Mothership is south, my Ion started flying up (+Z) and east). But, I couldn’t focus on it! I could select it through my Groups, but I could not force the camera to focus on it, so I could not even look at it. I only knew it was an Ion from the selection indicator in the upper right.
It would not surprise me if one of the defense ships is taking a similar action, flying off into nowhere - and thus avoiding being killed, preventing the mission from finishing.
EDIT 2: Failed to complete twice, started at the beginning both times. Both times, I followed the main/central path (the one with the Heavy Cruiser) all the way to the end, then came down to the station, resulting in my approaching the station from the side. Both times, the mission failed to complete. The third time, instead, after encountering the heavy cruiser (loaded a save here, did not start over), I immediately moved to a point just “behind” the station (protected side), without following the dust. This resulted in me approaching the station from the side which appears to be intended (the side with all the Defenders). Approaching the station from this main face (instead of from the side) seems to have fixed my problem, because the mission completed successfully this time.