This Bone Merger tool is outdated since the day it was released on the workshop, because of this, bugs like these are more likely to happen. I suggest you should get the Easy Bonemerge Tool, as the name suggested, It is A LOT easier to use than this tool.

Easy Bonemerge Tool:
https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=170917418&searchtext=East+Bonemerge+Tool