The Red Devils chief was furious at Clattenburg's failure to clamp down on what he felt were over-aggressive tactics from the relegation-threatened hosts, who recorded their first home win over United since December 1978.
"I told the referee what I thought - some referees don't like that. They don't like the truth," said Ferguson.
"But I just told him how bad he was in the first-half.
"I know Bolton are battling for their lives at the bottom but they were a bit aggressive and we were looking for some protection from the referee.
"The first half was just a shambles. It was foul after foul after foul. I felt they were over-physical and there were two or three really dodgy tackles. You hope the referee is strong enough to handle it. But he wasn't."
Ferguson was particularly annoyed at the treatment meted out to full-back Patrice Evra, who was on the wrong end of a series of firm challenges even if he was fortunate to escape being booked himself for a late tackle on Kevin Davies.
"I don't know whether they targeted him but the poor lad seemed to be involved in everything. There were some terrible tackles on him."