The 4th official had to get involved when a skirmish broke out as Gilligan came off in the 76th minute. It was alledged he struck or attempted to strike coach Jim Barron.
The player was clearly unhappy but boss Staurt Gray is trying to play the matter down.
"There were no punches thrown," Gray said.
"There was just a bit of an argument but it's all been sorted out now and there's no problem.
"The fourth official got involved and that made more out of it than there was. It wasn't bad at all.
"Ryan's kicked a bottle and he's done that because he's just frustrated.
"He was very disappointed and annoyed, we all are because it's a bad defeat."
All in all and very disappointing night for Northampton.