Yes, as suggested by your doctors it is possible to have this kind of a blister because of suture materials used at the time of amputation. Sometimes the wound discharges and slowly the body expels the suture material on its own. There is no risk as a result of this. Once the body has expelled the stitch, it would heal on its own.
At times in amputees, such blisters also form as a result of constant pressure from the prosthesis used. This pressure causes the skin to break down presenting as a blister or an ulcer. Until the pressure caused by the prosthesis is corrected it will keep coming back and wont heal.
At times, the pressure point is as a result of a sharp edge of bone protruding inside. This will have to be removed surgically. The diagnosis is very clear on clinical examination and if necessary an x-ray of the stump.
At times the wound can be as a result of infection in the bone. This will not resolve until the infection in the bone is controlled. Often infection in bone leads to fragments of dead bone which will have to be removed surgically. Until this is removed again the wound does not heal. The picture becomes clear only on an x-ray of the stump.
I am sure your doctors would have evaluated all this and got an x-ray of the stump before suggesting what he has suggested. Anyway I do not think there is a cause for worry (unless you are a diabetic, then in that case you need to treat the infection on a priority). The blister may have a nuisance value nothing more.