Three new cases lift the outbreak total to 888, and officials say to expect more.
The WHO said the attacks increase the risk of disease spread and are "profoundly disrespectful."
The attack is the second to target MSF treatment centers in just a matter of days.
The shuttered MSF center has admitted more than 600 people since December, 49 with confirmed infections.
Thirteen new cases raise the outbreak total to 872 cases, including 548 fatal ones.
The new Beni case is among 6 reported today, bringing the outbreak total to 859 cases.
Officials halted surveillance activities in Vuhovi after a nurse from Bisongo was killed.
Also, 3 new cases raise the outbreak total to 848, including 529 deaths.
The DRC warned, however, that travel between Beni and other affected areas could bring the virus back.
Five new Ebola cases were recorded in recent days, bringing the total to 840.
