you need to add another filter which can stop your assignment rule to fire everytime. For example, you donot want to fire this rule when case owner changes but project__c is true, change your assignment rule criteria to "Formula evaluates to true" and use below:

PRIORVALUE(OwnerId) <> OwnerId && Case.Project__c

you need to add another filter which can stop your assignment rule to fire everytime. For example, you donot want to fire this rule when case owner changes but project__c is true, change your assignment rule criteria to "Formula evaluates to true" and use below:

PRIORVALUE(OwnerId) <> OwnerId && Project__c

If you want to run your assignment rule only during creation of case use this formula.. ISNEW() && Project__c