Hi Rishi,
The energy will flow naturally that way ...equally through both branches of the fork in the sushumna. It isn't a problem and isn't something you have to control or limit. The important thing is that you are bringing your attention forward to the ajna at the end of the inhale with SBP. What happens with the prana is then simply what happens. It could be that everything flows up and out of the crown, or nothing at all, or a mixture of energy flows.
If you begin to experience any problematic symptoms, then that is a sign that you need to manage the situation in some way, otherwise carry on as normal and see it as a sign that things are working as they should.
Christi