I had this too for a while. From what I've been able to find I believe this is just a growth stage. Apparently some, but not all, hammers will do this at some point. It is believed to be a polyp fission stage that usually comes after the hammer is moved into more favourable growing conditions or a new tank.
Give it about a month and it'll go away and your hammer will be bigger and better than before. Mine started with one of those 'bubbles' and then 4 more showed up. A month later they were all gone and the hammer was huge. Don't poke at it or anything as you can damage the flesh and potentially kill the polyp while it's in this stressed phase.
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