In the The Lord of the Rings: The Two Towers, when Treebeard is carrying Pippin and Merry, Pippin asks to be taken south toward Saruman's fortress. But the maps of Middle Earth clearly show Mirkwood south of Saruman's fortress, so they would have to travel north to get there. Is there any explanation for this geographic inconsistency or is this an actual error?
Merry, Pippin and Treebeard were not in Mirkwood. They were in Fangorn Forest.
If they were toward the north of Fangorn forest, going south would indeed bring them past Isengard.
Your probably getting confused somewhere because Isengard is south-west of Mirkwood, not north.