Yes.
The calories you eat during the day to put on muscle are complex carbs and protein, and the carbs will either be used for energy or stored as glycogen in muscle cells. If you are eating properly, they will be very minimally stored as fat.
The calories you bust your ass burning doing cardio are different calories. They are fat calories from fat storage. They are not muscle building calories. However, if you do cardio at any other point during the day other than first thing in the morning on an empty stomach, they will not be fat calories, they will be muscle building calories or energy calories. This is why it is paramount that you do low intensity cardio on an empty stomach. Doing cardio with food in your stomach will get you in shape wind wise but will not burn fat at the rate you want.
If you take BCAAs before cardio you will only burn off a very minimal amount of your glycogen storages especially if you are doing low intensity cardio and those glycogen storages will be replaced during the giant carb heavy breakfast you eat right after cardio.