there is no "scene mode." Scenes are always available and you always use at least Scene 1.
whenever you call up any Preset, you call up Preset #xxx Scene 1. it's not a mode to turn on or something.
with default settings, and MFC-101 can be put into Reveal Mode - this changes Preset switches (default 1-5) to IA/effect switches. instead of choosing Presets, those switches now engage/bypass effects. the effects on switches 1-5 happen to be Scenes 1-5. so this is not "scene mode" by any means. calling it that will make things very confusing later.
regarding the original question: when you say "a scene came up" do you mean pressing a switch 1-5 made the MFC screen say "Scene x" (whatever number) and the Preset number stayed the same on the Axe display, but the Scene number changed?
if yes, then perhaps you did enter Reveal Mode and switched the Scenes like i described above.
did this seem to happen randomly? might you have pressed the Reveal switch on the top right of the MFC? did the switches select Presets at some point?
if you are sure you did not press the Reveal switch at any time, something else may be going on. i highly suggest a factory reset of the MFC, assuming you haven't programmed or setup much. the manual will tell you how to do that.
once you are at default settings, it will be much easier for us to troubleshoot if it happens again (assuming that you didn't press the Reveal switch).