At least part of the reason (and a more expert historian may be able to ascertain to what extent) was that the quality of McClellan's intelligence was substandard.

Allan Pinkerton, founder of the eponymous detective agency, was not especially suited to wartime espionage. While the Pinkerton agents performed well at more typical detective work, like identifying Confederate spies, when it came to estimating troop numbers their lack of military knowhow and willingness to uncritically accept rumours meant that the figures were often wildly inflated.

The opinion of many historians is that McClellan was predisposed to think himself outnumbered anyway, and readily accepted Pinkerton's estimates, even when they were clearly implausible.

Source: Bruce Catton, in Mr Lincoln's Army, is quite scathing of Pinkerton's efforts in this arena, and sympathetic to McClellan, while James McPherson is more critical of McClellan for unquestioningly accepting figures that were clearly inaccurate because they fit in with his conviction that he was outnumbered.