Four days after the game Preston amazed United officials by releasing pictures of the area used by Leeds showing three pieces of scrawled graffiti.
Jackson said of the alleged damage: "The lowest point in my footballing career was finding out about that."
The allegations of vandalism also stretched to claims the wash-basins in the dressing rooms were also damaged.
However, it is understood that there was no damage or vandalism when Leeds vacated the ground shortly before 11pm on Monday evening.
"It seems to be a case of trouble-making and sour grapes," said Ellis in the Yorkshire Evening Post. "The Preston people who showed me around were surprised and said they hadn't known anything about it until yesterday.
"There was some writing on the wall in the dressing room, we don't condone anything like that but otherwise it was in pristine condition.
"The writing could well have been done when the dressing room was cleaned after we had left."
United officials admitted to plastering their dressing room with notices saying "Billy Davies – Job Done" – a reference to comments made by the Preston manager after the drawn first leg.
Davies and his players had angered the Whites camp with their behaviour during the previous two meetings between the sides, and Monday's clash was a bad tempered affair.
Added to the dressing room allegations, Preston also claim that Leeds fans smashed seats in the away section on Monday.
"Once again the focus is on Leeds and our supporters, and it's not right," added Ellis. "People are trying to rubbish the club. It seems some just don't want the facts to get in the way of a good story."