Charges against the Dutch side also included the throwing of objects by fans and blocked stairways during Wednesday's 1-1 draw in the first leg at the Johan Cruyff Arena.
Tottenham were charged after a supporter invaded the pitch at their new stadium during their 1-0 first-leg win over fellow Premier League side Manchester City on Tuesday.
Both cases will be dealt with by UEFA's control, ethics and disciplinary body on May 16.
(Reporting by Hardik Vyas in Bengaluru; Editing by Ken Ferris)
