The Terriers chief was disappointed with some of the decisions which went against his side as Preston recorded a 3-1 success.
However, Cowley admitted that his side simply failed to start the game well enough, as Preston took a fourth-minute lead through Jayden Stockley.
They doubled their advantage before half time through Alan Browne before a penalty from Paul Gallagher took the game beyond Huddersfield.
Juninho Bacuna scored a consolation as Huddersfield lost for the first time since September 22.
"Of course a result like this is difficult to take, but I simply do not think we started well enough today, and that hampered us," said Cowley.
"We do have to praise Preston, they worked hard right from the start and we struggled to cope with them in the first half.
"They played with a real intensity and we found it hard to cope with that.
"We do not look for excuses in these situations as we cannot control things like the referee or decisions that may or may not go our way.
"I spoke to the referee at the end and there could have been decisions that went differently for us, but sometimes that is the way it goes.
"We have to look at ourselves now and look ahead to the next few games we have coming up.
"The travelling fans were fantastic today, but we let ourselves down with the performance. We came up short and we need to look at that together as a club."
Meanwhile, Preston boss Alex Neil was left beaming at the final whistle after seeing his side keep up the pressure at the top of the Championship table.
"I am really pleased, not just with today, but with our form in recent weeks," said Neil.
"Today is another three points for us, with three goals to go with it, and we stay unbeaten at home.
"I cannot have much to complain about now, we are getting results and performing well.
"It was important to go in at half time in front, and I think based on the chances we created, we deserved that.