Continuity mistake: When Mercedes flees through the forest to escape the soldiers, the blood pattern, thickness and color of blood on her face changes between shots. (01:33:00 - 01:35:30)
Audio problem: After the final skirmish between the partisans and Franco's Army, a riderless horse trots across the scene from right to left. The foley track uses the sound of a galloping horse (1,2,3 1,2,3) instead of a trotting horse (1,2,3,4 1,2,3,4).
Continuity mistake: When the Captain is stitching his facial wound, the camera pans down to Ofelia hiding by his table, revealing that there is no blood on the Captain's clothing. Seconds later, the Captain approaches the table wearing bloodstained clothing (from the earlier scene with Mercedes). (01:38:20 - 01:39:05)