The newly-promoted side traveled to Crewe's Mornflake Stadium for the League Two clash on Saturday afternoon, a contest that was relatively uneventful until minutes from the end.
It was then that the traveling Notts County fans were left furious six minutes into stoppage time when a penalty was given against their side following Jody Jones' adjudged handball.
With the referee pointing to the penalty spot, tempers boiled over among the County fans who made their feelings very clear to the awarding linesman in front of them.
The decision came after the match's original referee, Simon Mather, was forced to be replaced by fourth official Richard Wigglesworth after pulling his hamstring.
It was then alleged that Notts County's fans then started throwing projectiles onto the pitch before chanting word including 'cheat' and 'w****r''.
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This led to a lengthy stoppage when the assistant referee then refused to run the line in front of the away fans due to the close proximity with them.
The restart was then delayed even further when the other assistant referee refused to swap flanks with him due to having fears of his own about the abuse.
As a result, the match was delayed with Notts County's players trying to calm their supporters down, however it took 13 minutes before the match was in a position to restart.
Courtney Baker-Richardson stepped up for Crewe to take the high-pressure penalty and duly converted, giving the hosts a winner 19 minutes into stoppage time.
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Speaking about the penalty decision after the game, Crewe boss Lee Bell said: "Yeah I thought it was a penalty.
"I think with the new rule change when you are so close to it but in this day and age it is a penalty.
"I think he [the referee] got it spot on, it takes a lot of courage to do that after coming on because he took his time."