The fact that you and your spouse do not agree on custody does not affect a divorce application in Sweden. Although the issue of custody must be included in the divorce application, it does not influence the divorce itself.
If you both agree on who should have custody of the children, the court, as a general rule, will include the custody arrangement in the divorce decree according to your agreement. If you do not agree on custody, this issue will be resolved separately and will not affect the divorce application. The district court will grant the divorce regardless of whether you agree on the custody of your children or not.