Speaking on The Xtra Factor, the music mogul said: "I didn't know she didn't like the track. If she didn't like it, 100 million per cent I would have changed it."
Emily, 18, performed 'Wishing On A Star' for this week's Disco theme but said afterwards: "I really want to do something upbeat. I've just stood on the one spot."
She added on Xtra Factor that Simon was "so angry" with her for speaking out against him, adding: "He just saw me in the corridor, blanked me and said, 'we'll talk.'"
However, Simon said he wasn't angry with Emily at all. In fact, it was the opposite! "In a funny way I actually like the fact she showed some passion, that she cares and that she stood up for herself."
"Listen, I have a thick skin," he added. "I want her to be successful so we have to work very closely tonight and tomorrow to find the song we'll be happy with.|"
Simon said: "The way the process works is we choose the songs [on a Sunday night] when we get the jukebox [result]. We sit down, come up with some ideas and then routine them. Often we will change the songs if people don't like them – which does happen a lot. I didn't know, and maybe I'm wrong, but I didn't know Emily didn't like the track. If she didn't like it, 100 million per cent I would have changed it."
Next week's theme is Movie Week.
When asked if she'd be doing an upbeat song, Emily said: "I don't know but I don't want to promise anything! I'll try!"
X Factor airs Saturday at 8pm on ITV.