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Yellow cards were issued to Gillingham manager Steve Lovell and assistant boss Mark Patterson during a heated final few minutes at Southend.
Lovell and Patterson confronted the match officials after Gills' stoppage-time equaliser was ruled out.
Manager Lovell felt the decision to caution him was harsh.
He said: “I never swore, I just asked the linesman ‘are you sure it’s over the line?’ that’s all I said.
“He (the referee) said (I got booked) because I approached him and asked him the question, I don’t know how else I could have done it, have I got go into the stand?
“I asked him the question which I think any manager would do in that situation. I don’t think I did anything wrong but obviously if the referee thinks that then that’s down to him.”
Lovell, who was frustrated by the disallowed goal, spoke with referee Keith Stroud after the match.
The manager said: “He said he could only give what he could see and I said to him, ‘you know me, I don’t ever have a go at anyone or (normally) lose my rag."
“He said he understood but that you can’t talk to the linesman like that. I don’t know what I was meant to say, I just asked him a question, ‘was it over the line?’
“I didn’t swear, I never swear, that must have been my first yellow card in 40 years.”
It’s a second booking of the season for Gills’ assistant manager.
Patterson made history by becoming the first member of Gills’ coaching staff to fall foul of the Football Association’s new tougher disciplinary rules introduced this season for misconduct in the technical area.
He was booked along with Peterborough United manager Steve Evans during the league game in September.
Four bookings lead to a one-match ban with further yellow cards leading to a misconduct charge.