The hosts took the lead in the first half through Leon Legge despite appeals for offside amid claims the ball brushed a Gillingham player's head, which resulted in a flag from the assistant - subsequently overruled by Williamson.
Dagenham battled back and at the second time of asking, Femi Ilesanmi hammered his side level soon after the break.
But three minutes after coming off the bench, Deon Burton tucked home his 11th goal of the season after Daggers keeper Chris Lewington was adjudged to have brought down Anton Robinson - another decision Still disagreed with.
"Two mistakes," he said.
"The linesman says he's headed the ball, all our players say he's headed the ball, the referee says he didn't see him head the ball and the linesman's seen it.
"For the penalty, the referee says he hasn't seen that the fella got brought down, he can't have it both ways.
"We can't affect that we can only affect what we do, but without a shadow of a doubt I don't mean to have a go at referees because it's the hardest job but when they look at the DVD they'll realise it's two mistakes.
"The thing that disappointed our players was that their player said 'I headed it' but as I said we can't affect that. The referee is never going to change his mind but I understand frustration creeps in but you can't change it."