One possible explanation is that the animators accidentally inverted the ATK/DEF values of Kuribandit", giving it an ATK of 700 when making the calculation. It must be noted, however, that in the anime, its ATK/DEF values are never shown on the screen (for both English and Japanese versions), making its true statistics a bit of a mystery.
Another explanation is that in the anime, Eatos must send an Equip Spell to the Graveyard to activate its effect, like the real-world card. With the 300-ATK loss, Eatos's ATK changes from 3300 > 3000 and then 3000 > 7000 due to its effect. However, the sword is destroyed after the attack is thwarted, for dramatic effect.
Yami manages to defeat Eatos by combining "Timaeus" and his "Dark Magician". Rafael screams in anguish as his monster is destroyed. Rafael, in horror, sees Eatos smiling at him as it flies into the heavens. (In the dub, Rafael cries out afterwards that nobody sends his "Guardian Eatos" to the Graveyard.) Rafael suddenly lowers his gaze, and the whole Seal begins to "pulsate", evidenced by the sound made and the rippling effect of the invisible dome the "Seal" creates. Even Rafael's crest flashes red from time to time. Rafael claims that his "Eatos" is just sleeping in the Graveyard, but she will come back in a new form as she is immortal (in the dub, Rafael claims that when a monster of light and purity like his Eatos is destroyed, it is replaced by a different creature: a creature of darkness).
A crevice opens on the ground and a horrific vision comes out: "Guardian Dreadscythe". It itself is the personification of Rafael's dark side. He then ruthlessly sacrifices his other "Guardian" monsters to increase the ATK of "Dreadscythe".
Remembering Yugi's words, Yami plays a Continuous Spell Card to allow Rafael to "see the Monsters which you've sent to the Graveyard". A purple fog forms as the Enochian symbols on the rim of the "Seal" spin, and it covers the whole dome from the outside.
Yami Activates Trap Card "Rope of Life": He Discards his entire Hand to Special Summon "Kuribabylon" back to the Field in Attack Position with an extra +800 ATK (1500 → 2300 ATK / 200 DEF). (NOTE: at this point, Yami's Hand was 0, so he didn't need to Discard any Cards from his hand.)
When "Guardian Dreadscythe" is Summoned, Rafael can Equip it with 1 Equip Magic Card from his Graveyard. He chooses "Reaper Scythe - Dreadscythe", which gives it +500 ATK for each Monster in his Graveyard. There is currently one in Rafael's Graveyard, so "Guardian Dreadscythe" gains 500 ATK ("Guardian Dreadscythe": 3000 → 3500 ATK / 2000 DEF).
Draws Spell Card "Card of Sanctity" and subsequently activates it to make him and Rafael Draw until both have 6 Cards in their Hand (NOTE: The real-life version of the Card allows you to remove every Card from your Hand and on your Field then you Draw until you have 2 Cards in your Hand). One of the cards Yami just Drew was "Watapon". This allows him to Special Summon "Watapon" immediately to the Field (200 ATK / 300 DEF) in Attack Position.
During the End Phase of Rafael's Turn, the other effect of "Magical Pigeon" activates, destroying all remaining "Pigeon Tokens" and Special Summoning "Dark Magician Girl" back to the field in Attack Position.