Unless there is a ticking time-bomb, it is assumed the scene ends immediately after combat (and yes, I know that Modiphius is kinda all over the Place with Acts, Scenes and Encounters in their published Adventures). With the exception that if someone is dying, the PC have a chance to give First Aid just before the Scene Ends and everyone recovers their Stress.
A new Scene starts whenever the GM feels it is appropriate. It should also fit in the narrative. For example, if an away team beams aboard another vessel and tries to seize the bridge, fighting breaks out. After the fight, if all enemies are defeated and the bridge is under control, the Scene should end because it fits narratively. On the other hand, when the away team has to run through various corridors and decks to get to the bridge, I (as a GM) would not end the Scene after each skirmish in a corridor.
As a rule of thumb, Scenes only end (and Stress therefor regenerates) if the characters can take a few minutes to catch their breath without an immediate danger.