GameObjects not being deleted in new Scene [SOLVED]

Not sure if this is a bug or I changed some settings. All of a sudden gameobjects from the previous scene remain in the next scene. Its also very strange that another scene gets loaded and there is absolutely no line in the script that tells the game to load another scene…

Either I’m going crazy or something is wrong with Unity xD
Any suggestions?

EDIT SOLUTION:
Not sure why but for some odd reason the two scenes were being fused together…hard to explain what happened. But I managed to fix it by calling the Application.LoadLevel() in my OperationResponse (if you are familiar with Photon server or even Unity Networking)…and then having a separate game object in the next scene determine whether to instantiate a new player. (This is based on a simple boolean variable whose default is true on a new game and when the player enters the map, it becomes false. If the player leaves the game but does not close the application (eg. by logging out), then the boolean is reverted to true before the player can re-enter the maps).

Please show here the line of code that allows changing scene.
And check if you don’t use this : http://docs.unity3d.com/ScriptReference/Object.DontDestroyOnLoad.html

If you Instantiate your objects when launching the scene, make sure you didn’t copy/use the same scripts for scene1 and scene2.

I guess this is also the reason your scene doesn’t get loaded to the next scene, because you used the same script in scene1 as for scene2.
(example : When you were in scene2 you clicked on a button, the function of that button is to get you to the next scene called scene3. But because you used the same script for scene1 as for scene2, you instead get loaded back into scene2)

Go to scene2 and make a new script, copy your old script and paste it into the new script, change the name of the loadlevel into your next preffered scene and delete the old script in scene2 from the hierarchy

Application.LoadLevel ("PrefferedSceneName")