A scene is a part of play that occurs within the game world in a single place for a continuous period of time. A session will generally include multiple scenes. Establishing a scene (i.e. when and where it takes place, and which characters are present) is usually, but not always, the province of the GM.
The term is often used synonymously with encounter, but while it is common for one scene to feature exactly one encounter, that is not always the case. An encounter might last longer than one scene, particularly if it lasts a long time or has the player characters changing location. Similarly, a scene might include more than one encounter. Scenes are more clearly delineated than encounters, as it is clear that any change of location or time skip indicates the end of a scene.
Some rules may indicate that certain events of actions can only happen a limited number of times per scene (often once per scene). Because scenes can last for an indefinite period of time, such limitations can have significantly different impacts on groups with different play styles (or even from session to session), and as such should be used carefully or not at all.