I'm normally a fan of Hank and John Green's YouTube empire. Granted, their Mental Floss channel occasionally gets things wrong or at least wrong enough that one can reasonably complain about it, but rarely do they commit an error of the magnitude here, about something that ought to be common knowledge for any American middle school student. It's something I've written about before (link) when electoralvote.com got it equally wrong. Here's the bit in question (about 30 seconds):
Link (to full video): https://youtu.be/NS4FhUmuTnk
Host Elliott Morgan erroneously claims that it's a "misconception" that Lincoln's Emancipation Proclamation freed any slaves because it applied only to the areas in rebellion, and, also erroneously, claims that it applied to the rebellious states because "Lincoln wanted to hurt" them.
The only part of this that's right is that the Emancipation Proclamation applied only to regions of the Confederacy still deemed in rebellion (and not, for example, to the four slave states that never left the Union or to the regions already back under federal control, such as New Orleans and the surrounding area). But that limitation was a matter of legal necessity. The president of the United States is not a king and can't rule by decree. In fact, during the Lincoln-Douglas debates Lincoln had pointed out that even Congress had no clear constitutional basis for outlawing slavery in the several states. (The territories, being under direct federal governance, were another matter.) As commander in chief, however, Lincoln did have the authority under the Law of War (and the Confiscation Acts of 1861 and 1862) to order the seizure of enemy property in furtherance of the war effort. The Proclamation hence inter alia ordered federal troops to seize chattel slaves (which were legally property -- that's what "chattel" means) and grant them manumission.
On the very day the Emancipation Proclamation took effect, the first of 1863, Union troops in de facto control of areas still deemed in rebellion freed about 50,000 slaves, and as troops advanced further into the South, the officers carrying printed copies of the Emancipation Proclamation, they freed thousands upon thousands more. By mid-1865 almost all slaves in the Confederacy had been freed. In December 1865 the 13th Amendment was ratified, freeing (at least de jure) the remaining slaves, including those in Kentucky and Delaware, at that point the only remaining Union states that had not yet outlawed slavery. But at that point the great majority of slaves had already been freed by the Emancipation Proclamation.
In fairness to Elliott Morgan, the blame lies not solely with him but with whoever wrote the episode and with the "fact checker" listed in the credits, and for that matter everybody in the room who had a chance to speak up and point out the glaring Fox-News-level mistake. This is a fundamental piece of American history and no graduate of an American middle school should get it wrong.
(Updated 2015 June 24 and 2018 January 29 to add a few additional details and try to improve clarity.)