The Iron never recovered from David Clarkson's 13th-minute opener before Nicky Maynard added a second.
"We gave away two extremely poor goals and looked as though the first one knocked the stuffing out of us," said Baraclough.
"Maybe games are catching up with us and perhaps I should have made some team changes. I thought the players looked alright in training on Friday and I thought we would play a lot better."
The Iron arrived at Ashton Gate in the midst of a fine run of results which had seen them take seven points from their previous three outings.
Those games were all at Glanford Park, but they could not extend that to their away form.
The Iron failed to reproduce the desire that saw them come back from two goals down to beat Sheffield United 3-2 on Tuesday.
"What's the difference between coming back from two goals down against Sheffield United to win in midweek and being two down against Bristol City?" said Baraclough.
"The difference was that while we showed belief that we could recover against Sheffield, here we never looked as though we might get back in to the game.
"It was a poor performance in an important match after some improved results had given us all hope."
Source: PA