I had this happen once and it took a while to figure out. It was a combination of not using sterile water when i mixed the GA3 and spraying during ¨day¨ time. Water on plants during the day is like a magnifying glass and will sunburn / damage the tissue. The tissue damage greatly increases the chance of picking up bacterial / fungal pathogens in the air and from the solution.
If the stock or scion were already infected it would have shown up before now and would have greatly affected the base area (soil line) of the stock. This is easily noticed because it causes the main stem to wither starting at either the soil line or the scion junction.