If you can remove the rocks with bubble algae and place them into a bucket, you can pick off of the bubble algae in the bucket. Make sure you get every little bit of it off. Then rinse the rock off with tank water or fresh saltwater before putting it back into your display tank. That will rinse off the spores.
I have also had a bubble or two come in on a new coral purchase. These were attached to the rock that the coral was attached to. I took lighter and burned off the bubble algae with fire, scraped the rock, and rinsed with tank water. This works!