For Project Contract Line Milestones you need to manually calculate the price for the milestones. In most common cases the milestones are like:

1. 20% of the Total amount before start of the project
2. 50% of the Total amount at the beginning of the project
3. 30% of the Total amount at the end of the project

It would be an added functionality if you can add a Project Contract Line Milestone and add the Percentage in a field and let Dynamics365 calculate the price and fill in the price.