The word 'mal' means 'bad' or 'poor'. 'Malalignment' implies that the relationship or geometry of one bone in relation to its neighbouring bone is outside of what one might consider normal.
This may be due to soft tissue issues or bony problems.
"....Patellar malalignment (PM) associated with knee pain is common in all age groups, and the most common predisposing factor is imbalanced peripatellar soft-tissue tension...."
Usually this is a varus malalignment or a valgus malalignment.
"....Varus alignment shifts the load-bearing axis medial to knee center, creating a moment arm that increases forces across the medial compartment and reduces lateral load; the lateral shift of the load-bearing axis due to valgus alignment increases forces across the lateral compartment and reduces medial load....."