There are some mistakes that people make that can cause damage during the flow of Qigong: Overdoing a movement beyond your physical capacity, especially with a previous injury, for example to the spine, can result in physical injury or aggravate the injury.
Not using intention when making a movement can result in energy deviation.
For example, waving your arms around, circulating the Qi and dispersing it, instead of directing the movements appropriately with your mind.