United have been held to two draws in the space of three days either side of Christmas, conceding a late goal in their 2-2 draw with Leicester City last weekend before needing a stoppage-time strike of their own to share the spoils with Burnley on Boxing Day.
Premier League leaders City have an extra day of rest before taking on Newcastle United on Wednesday, and Mourinho believes that the fixture list favours Pep Guardiola's side.
"I'm not just talking about the privileged runs with six days to recover and enjoy and to prepare but ones with a little bit more than us," Mourinho told Sky Sports News.
"For example the ones with a little bit more rest, like one day. The extra day means a lot because it means they aren't working [on Christmas Day], means they can be back to work and be ready for the next day.
"The problem I see here is the difference between some teams."
United, who face Southampton in their final game of 2017 on Saturday, could fall 15 points behind City at the top of the Premier League table should Guardiola's side rack up an 18th successive win tomorrow.