After a goalless first half, Robin Shroot edged Boro ahead in the 55th minute before a quick-fire double turned the contest on its head.
Hope Akpan slotted home on the rebound after 65 minutes before Dannie Bulman's 69th minute strike took a wicked deflection and left Stevenage with just one win in six games.
Smith said: "I'm bitterly disappointed. We deserved more than we got. Going a goal up at home as well, which hasn't happened too often.
"We created enough moments, got in enough good positions, but the goals, I have to say, were pretty soft, avoidable and in the end have cost us.
"I thought we opened up slightly the brighter and looked a little bit more forceful with our play in the opening exchanges in the second half. And the goal gave us a big lift, and honestly I thought we would go on and win the game from there.
"We've finished the game with plenty of pressure and some good moments. The goalkeeper made a cracking save at the end. We had numerous chances on the edge of the box, on a very tricky surface to get shots on target.
"Players that we have leant on massively, Greg Tansey, Lucas [Akins], have fallen short of the quality in front that we've seen them produce before."