I don't have FTM but it sounds like you have the same record linked to both of them. Perhaps when you entered the second one something popped up to ask did you mean the one you already had. Pressing enter/return would probably have confirmed it.
Does FTM display it's record numbers? If so, then a quick check would be to see if these are the same. Otherwise perhaps try listing individuals and see if you have one or two entries for this name. If there are two, it may be that one is linked twice and the other not at all.
In FH (Family Historian), every time I enter a child I have the choice to select an existing member of the tree or enter a new one. I can unlink people from their parents, if necessary, and recreate the links between them. It sounds like you will need to do that for this record.
Perhaps someone familar with FTM can give more precise help.