Mark made the comments while being interviewed by Andy Cohen on Watch What Happens Live on Thursday night.
Jennifer starred with Mark in 2004 comedy 13 Going On 30, and Andy asked Mark if the pair still keep in touch.
'We had a great time together, and I think we would' he revealed.
Adding: 'But then Ben came on the scene. And that was the end of that.'
Andy then asked Mark a made-up question to provoke a response, asking: 'I heard he doesn't allow her to have male friends?'
However, Mark refused to confirm nor deny the statement, shrugging instead, suggesting some bad feelings between the pair.
Andy then admitted that he had 'made-up' the suggestion that Ben doesn't allow his wife to have male friends, prompting yet more awkward silences.
Mark was promoting his new movie Begin Again with his co-star Keira Knightely.
Keira was seen scrunching up her face at one point, as Mark held up his hands and refused to comment further about his beef with Ben.