What was the basis for your initial conclusion that you 'saw a couple of outliers?'
How much did the results of your regression analysis change? In what way did they change?
Also, how many observations do you have? How many predictors did you use in the model? Are any of them collinear with others? Does your model include terms as transforms like square (X^2) or crossed (X1*X2)?
Cook's D is based on the sum of the differences for every observation between the predicted response using the full data set and the predicted response using the leave one out set. So one or two highly influential observations might not result in a large Cook's D if there are many observations.