County are still supporting a significant wage bill and Ray Trew took over the club to keep them afloat and steered away from potential administration.
But Stewart is baffled as to why the League Two Champions have gone unpunished.
"When I remember the barbed wire fences we had to get through in order to get back into the Football League, it puzzles me that there has been no punishment in this case", he said.
"It's not for me to say what that should be but I have to say that we are not happy about what has gone on at Notts County and other clubs in the league feel the same."
Several clubs in the division are thought to have raised an issue with County's funding throughout the season.
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