Terriers goalkeeper Alex Smithies saved a 16th-minute penalty from Daryl Duffy but could not keep out Jeff Hughes' spot-kick seven minutes from time.
"I played the wrong system. I hoped that by putting three in midfield we would dominate their two and get a foothold in the game," said Clark.
"But it didn't work and by the time I changed it Rovers were playing with confidence and had taken a grip. I hold my hands up, but the players didn't do the nitty-gritty you need to win away games.
"We didn't pass the ball as we can and played too many long balls. We did ask a few questions in the second half, but there are no complaints."