That he failed to pursue Lee after Antietam.
US President Lincoln believed that General George B. McClellan could have easily supported and reinforced Pope's Army of Virginia. Lincoln and members of his cabinet believed that McClellan was trying to purposely allow Pope's troops to face a defeat.
President Lincoln's preliminary Emancipation Proclamation in 1862 was a shock to General McClellan. He also was shocked when Lincoln soon after suspended habeas corpus. He was opposed to both of these actions by President Lincoln.
When General George B. McClellan returned to Washington DC on March 11, 1862, he became aware that President Lincoln removed his title of general in chief.
Lincoln's response to General McClellan's command was that Lincoln relieved McClellan of Command.
As the Union's Peninsula campaign was in its early stages, General McClellan was certain that President Lincoln was hampering McClellan's war operations. Lincoln had stepped in and retained the corps under General McDowell to defend Washington DC. Lincoln believed this was a necessity.
General George Mcclellan was, by all accounts, an egomaniac. He was bitter over his removal from command by Lincoln. In running for President in 1864 against Lincoln, he sought to "get even" and embarrass Lincoln.
On October 13, 1862, President Lincoln sent General McClellan a long letter explaining the plans Lincoln believed were needed to defeat the South. Lincoln was almost sure that an aggressive Union response from McClellan's army would not be forthcoming. With that said, McClellan had every chance to keep his position if he even tried to execute the plans Lincoln sent to him.
President Lincoln did second guess himself for a while. This is because General McClellan had years of extensive industry and military experience. Lincoln, however, would soon find a replacement for the ousted General.
After General McClellan had persuaded President Lincoln to agree to McClellan's Peninsula campaign, he began shipping troops of the Army of the Potomac to Fort Monroe in April of 1862. By April 3, 1862, President Lincoln was deeply concerned that McClellan had planned on leaving less than 20,000 troops to defend Washington DC as his forces began to occupy Fort Monroe. Lincoln refused to let the Corps led by General McDowell to join the rest of the Army of the Potomac at Fort Monroe. Lincoln ordered McDowell to stay near Washington DC as a defensive measure. This began what would be an ongoing dispute between McClellan and President Lincoln and Secretary of War Stanton regarding the troop levels McClellan wanted for his campaign to take the Rebel capital of Richmond.
On April 3, 1862, US President Lincoln is upset that General George B. McClellan has left less than 20,000 troops to guard Washington DC. McClellan was concerned about his Peninsula Campaign. Lincoln refuses to allow any of General McDowell's forces to join McClellan. This causes a rift between Lincoln and McClellan.
he had refused to lee's retreating army into Virginia
On April 20, 1862, General George B. McClellan informed President Lincoln that Robert E. Lee was replacing the wounded General Johnston. McClellan also mentioned that this change was good for the Union as Lee was known to be weak and timid.