Just let it go. Over time, as it grows, it will encrust under the frag then back out onto the rock. Then, as it continues to spread and get bigger, it will also start grow its skeleton beneath the flesh. Unless the gaps between the plug disc and the rock beneath are really bit, the skeleton should eventually fill in the gaps around the plug.
Of course this will take quite some time. So, if you're impatient you'll need to reposition so more of the coral and plug are in contact with rock ... or you could remove some of the coral and glue directly onto the rock. But, if it's already encrusting most of the top and bottom of the disc, you'll be throwing away a lot of the growth you've already got.