Fiskbit is correct. The technical explanation is as follows;
Each unit in the game has a hidden attribute that keeps track of when it was created. Scout intel shows all the ships on the planet that were created up to the time that you scouted the planet. Therefore, the number of ships may fluctuate according to the destruction/travel of any ships that were in existence before you scouted the planet, even if no scout is present.
Proper intel 'snapshots' are on the Future DLC list.