Dortmund have been charged with stairways being blocked, while Liverpool face a charge in relation to their supporters letting off fireworks at Signal Iduna Park.
The cases will be dealt with by UEFA's control, ethics and disciplinary body on May 19, the day after the Europa League final in Basle.
Liverpool already face charges of illicit chanting, setting off fireworks, throwing objects and more general crowd disturbances by their fans from the second leg of their previous round against Manchester United at Old Trafford.
United have also been charged with crowd disturbances and throwing objects, in addition to blocked stairways.
UEFA are still investigating claims Hillsborough and Munich songs were sung by rival fans at both Anfield and Old Trafford during the last-16 tie and further charges could yet follow.
Source: PA