Are your great-grandparents listed in the index twice? If not, the program is not entering them a second time; it is just displaying a second relationship in some screen or report that you are looking at. Which means you either have 1) a relationship messed up somewhere or 2) our great-grandparents really are related to someone on your mom's side.
Just exactly what report are you looking at? Are you looking at an ancestry screen / report of yourself? or a descendant report of one of your mom's ancestors? It would be helpful to know where it is that you are seeing what appears to you to be a duplication, or what it is that makes you think they are related to your mother.
Tools or screens that FTM has that can help you analyze the situation are:
1) Relationship View of Person Tab of People page
Relationships button in upper right corner "flips" between the "Facts" view and "relationship" view.
Check each person's parents and other relationships, and which ones are preferred.
2) Relationship calculator (Main Menu > Tools)
Set your uncle, yourself, etc as the "top" person and the others, one at a time, the bottom. If related more than once, look under the down arrow button.
3) Main Menu > Person > Attach / Detach
The DETACH part of the attach/detach is where you can see all families a person is a part of, as a father, spouse, or child. This is the part of the program where you attach people already in your file to each other (or detach them).