Justin Edinburgh said his players were hurting after their winning run was ended in controversial circumstances.
Yeovil grabbed a point from the League 1 clash after Adam Morgan scored from the penalty spot.
The hosts were handed the chance to level the game when referee Simon Hooper awarded a penalty following a coming together between Gavin Hoyte and Joel Grant.
“It certainly wasn’t a penalty and I am sure the referee won’t sleep very well tonight,” said a frustrated Justin Edinburgh.
“The players are hurting but it was a valuable point.”
Moments before Yeovil’s stoppage-time equaliser the Gills thought they had won it when Luke Norris scored with two minutes of normal time to play.
His goal followed one from John Marquis as the Gills bounced back from a poor opening half.
“To get ourselves in the position we did, after a slow first half, we feel very hard done by to have not got three points,” said the Gills boss.
“I was disappointed and I wasn’t happy with anyone really. I thought we were well below the standards we have set.
“I said at the start of the week this would be a difficult place to come to, they are fighting for their lives and this was going to be a test. We passed most of the questions posed to us but we certainly need to be starting faster than we did.”
Edinburgh made a change of personnel and changed formation in the second half. Both helped get the Gills firing.
“Our better players were in defensive areas and we needed to push one of those up further,” said Edinburgh.
“We took Danny Galbraith off and put Jermaine McGlashan on, who would certainly stretch us, and take the game to them, which he did. That allowed Bradley Garmston to get on at them the other side and I certainly felt we were more effective second half.
“We said at half time, if we are going to surrender this (unbeaten run) let it be because a team have outplayed us and been better than us, rather than us being below that standards we have set. I think they responded to that in the second half.”