Factual error: When everyone went up in the hot air balloon the sun and the moon are both visible. The illuminated side of the moon is facing in the wrong/other direction from the sun, which doesn't work.
Tim and Xandir, Sitting in a Tree... - S2-E11
Continuity mistake: When an Entertainment Weekly magazine falls onto the table and Foxxy and Clara both hold it. If you look at Foxxy's hand you see that her furry bracelets suddenly disappear and then reappear.
Tag Team Trial: Part 1 - S1-E10
Continuity mistake: Jaden fuses together Elemental Hero Burstinatrix and Elemental Hero Clayman to summon on out to the field Elemental Hero Rampart Blaster. As the monster's being summoned to the field, Jaden calls out the name and says "Beat that." As he says this, he extends his arm and the finger that is shown to be pointing is pointing slightly downwards. In the next shot, as Elemental Hero Rampart Blaster appears on the field, his finger is suddenly perfectly level with the rest of his arm. (00:15:40)