I have shared hosting and domain maindomain.com and i have hosted around 7 addon domain. i can see google is indexing link like addon1.maindomain.com, but i have registed a seperate domain like addon1.com. So google should index only addon1.com. Thank You Balaji.
google somehow found that link but once you start building links to the new domain, your new domain will get indexed. what you are seeing is only temporary and nothing to worry about.