So, I touched on this a bit during the Civil War panel a few months ago. Check out my response to a similar question here: https://www.reddit.com/r/AskHistorians/comments/3c73kh/panel_ama_the_american_civil_war_era_military/csteh1h.

TD;LR - McClellan trusted his spymaster, Allan Pinkerton, far more than he should have. Pinkerton was a great detective, and a tenacious, mean-spirited man (so one would think him ideally suited as a military spy), but he never got the hang of proper espionage techniques when it came to evaluating an enemy's strength. He trusted in rumor and scuttlebutt too much, and had no real experience acting as a war-time spymaster (hence is over-exaggerations of enemy forces). This fed into McClellan's already overly cautious nature, and was further reinforced by McClellan's staff, which was rewarded for loyalty (not candor).

At Antietam? They weren't that wrong.

Whilst the Pinkerton numbers, Comte de Paris numbers and McClellan numbers are generally high, they were typically 20-33% high. It's worth noting the numbers are usually "aggregate present" and numbers are often for the whole Virginia theatre, including West Va, Yorktown, Norfolk and Richmond as well as the valley etc. A major mistake often made is taking McClellan's estimate of the whole Virginia theatre and comparing it with a fraction of the rebel force. It's worth remembering the most complete returns we have (December 1861) show 118,306 Confederates present in Virginia (inc. Norfolk), and this misses troops at Richmond and in West Va.

On the Peninsula his numbers were almost spot on. He initially estimated 18-20,000 at Yorktown (actually a bit under) and on 7th April upped this to 30,000 (about right), and on the 20th April wrote Burnside advising him that the enemy had concentrated their main body at Yorktown with 80,000 men (very accurate).

Around this time Lincoln opens a dialogue with McClellan about manpower, and insists on measuring McClellan's army by the "aggregate present and absent" - McClellan forwards some reports from Pinkerton that clearly use the same metric (estimating 100-120,000 rather than the 80,000 McClellan communicated to Burnside a few days earlier). Note that using that metric Pinkerton is about right.

Now, almost two months later at Richmond Pinkerton's numbers have started to diverge from reality. He has a table of regiments with the enemy army, but it has 36 infantry regiments listed that weren't with Lee's army (up from 7 two months earlier). A few of these are at Petersburg or SW Va., but most are out west or in the coastal garrisons (or didn't exist, like the 65th Va). These add a large number of extra troops to the estimate. If you follow Pinkerton's maths through (700 present per regiment) with the extras and assume that he counted battalions as full regiments the numbers resolve at 180,000 - exactly what Pinkerton said after they realised the rumour of 20,000 from Beauregards army coming up was just that (remember McClellan himself doubts it). Thus we have an overestimate. Using a bit of maths we find that by the "aggregate present" measure Lee probably had about 135,000 during the Seven Days (c.f. Harsh and see a regression plot of mine here: http://67thtigers.blogspot.be/2015/08/effective-vs-present-for-duty-1-army-of.html

Thus the estimate of 180,000 is about 33% higher than reality. This had happened whilst at Richmond, not before.

At Antietam we have an estimate that is essentially spot on except it adds 46 regiments whose formations are unknown (remembering Lee's aggregate present was ca. 90,000). Confusion really kicks in because the rebs straggled heavily and probably didn't have half of their men available at Antietam. Remember the first full return after Antietam (20th October) gives a strength of 79,595 present. Thus McClellan's estimates of 100-120,000 are not a phantasmagoria, but rather a misidentification problem with 46 regiments extra....