It varies quite a lot but more common than you might think. Medieval conflicts in Europe basically consisted of three distinct types of warfare: pitched battles, castle sieges and raiding/scorching lands.

Pitched battles were relatively rare, at least compared with ancient and classical times, because both sides were very aware of how decisive they could be. As these were clashes between two armies civilian casualties were relatively low, but each army would travel with a baggage train and a whole load of non-combatants to manage this (cooks, merchants, priests and so on) who could either be caught up in the fighting, as attacking an enemy's camp was a good way to distract them from their battle plan, or massacred afterwards if one side had comprehensively won the battle itself.

Castle sieges, and sieges of walled towns, were often much more frequent. Many of these eventually changed hands with relatively little bloodshed after a siege (often the defending force would set an arbitrary deadline for a relieving army to arrive by, and if none appeared in time would open the gates and hand over the castle) but in cases where defenders refused to submit they might be killed en masse once a siege succeeded. Death from starvation or illness during sieges would also likely take as much of a toll on the civilians as the military inside the walls.

Harrying the land was a common tactic used by armies on the move, often by spreading out into a wide line of troops and burning and destroying any crops and buildings in their path, either to try and force an opposing army into a battle, or the reduce the resources available around a settlement or fortification. Civilians caught in the line would often be either made to flee or killed outright. Raping and pillaging was commonplace even if ostensibly frowned upon in some cases. Harrying territory was used almost as much by retreating armies as attacking ones - especially if those in retreat were fighting on home territory (such as France for a large part of the Hundred Years War) to reduce the available resources for the pursuers and try and slow their advance.