McDonald put Gillingham ahead straight after half-time with a stunning overhead kick, but the Gills looked to have thrown it all away in the closing stages.
McDonald grabbed a point for Gillingham with a run and finish deep into stoppage-time, but Taylor admits they cannot afford to concede so many goals.
"We can't feel sorry for ourselves for conceding late goals again," he said.
"That's football. If you make wrong decisions you'll get punished. At times, we're doing that, and we can't keep doing it.
"I don't feel we're having a great deal of luck either, considering certain injuries we're getting, and we hit the crossbar twice.
"Two clean sheets this season is not good enough. We've got to get better than that.
"Cody McDonald was back to how I know he can play. He was great , he looked a goal threat.
"I think he's getting more and more confident playing against defenders. The first goal he took exceptionally well and he was alive and alert for his second goal.
"Scoring early on helped the players' confidence,and although we conceded two goals, which were very poor on our behalf, we never stopped and the players deserve a lot of credit for that."
Gillingham almost won it through McDonald only for goalkeeper Richard O'Donnell to save well with his feet.