The 'On The Floor' hitmaker - who called time on her seven-year marriage to the singer last month - was reportedly hoping to send the couple's three-year-old twins Max and Emme to a specialist Scientology school, however Marc wasn't so keen on the idea.
A source told the Mail on Sunday newspaper: "Jennifer and Marc couldn't see eye-to-eye on the subject. She's always been more into the church than him. He wasn't a huge fan and it caused problems."
The 42-year-old star recently admitted she wished people would judge the Scientology religion - also followed by Jennifer's close friends Tom Cruise and Katie Holmes - before they know what it is.
She said: "I just wish that people wouldn't judge it without knowing what it is."
Despite the couple's shock split, Jennifer claimed she will remain an "eternal optimist", and is still confident about finding love again.
She recently explained: "This was the hardest decision I've ever had to face. I really wanted this family to work. That was my biggest dream, and I worked hard at it. We both did. Sometimes it doesn't work - and that's sad. But I remain an eternal optimist about love. I believe in love...It's still my biggest dream."
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