Audio problem: When Philippe climbs up to the grating in the church, a little girl talks to him, but her mouth does not move.
Other mistake: Just after Isabeau falls from the abbey tower and turns into Ladyhawke, a soldier emerges onto the roof of the tower and questions Phillipe. An arrow is then fired (by Navarre) into the left-side of the soldier. However, he initially grabs at his right-side. After a couple of seconds he correctly grabs at his left-side, before falling off the tower. (01:00:26)
Continuity mistake: After Philippe the Mouse escapes from the prison and has swam out the underwater grate hole, another scene shows soldiers riding through the peasants leaving the castle to search for him. In the background, two soldiers can be seen sitting by the moat, eating. One stands and grabs suddenly around his belt, obviously looking around for something. A while after this in a separate scene, Philippe the Mouse is shown surfacing in the moat behind these two soldiers and grabbing the knife from beside one of them and slicing away a cord on the soldiers belt and stealing his coin purse, then swimming away quietly and saying the line about 'I know I promised not to steal Lord, but I know, that you know, what a weak-willed person I am...' Obviously the scene with the soldier standing suddenly and discovering his missing coin purse should have come after the actual 'stealing of the purse' scene.
Continuity mistake: Just a few nights before the solar eclipse, a shot of the full moon is shown. Only 1 or 2 nights later, a clear quarter moon is shown. A quarter moon would appear more than a week after a full moon (not 2 nights) and a solar eclipse can only happen during a new moon, which would be a week or more away from the quarter moon, even though in the movie it happened the next day.
Revealing mistake: When Philippe the Mouse is caught by the Bishop's guards after he has escaped from prison, Navarre shoots an arrow into one of the guard's arms to stop him cutting Philippe's throat. If you look at the spot on the guard's upper arm where the arrow will hit just as Philippe says 'May God have mercy on my soul', you will see that there is already a hole there - even before the arrow hits him.