The On The Floor hitmaker - who ended her seven-year marriage to the singer in July - 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 wouldn't judge the Scientology religion - also followed by Jennifer's close friends Tom Cruise and Katie Holmes - before they know what it is.
PHOTOS: Jen and her Men
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."