There are several clusters of the little insects scattered throughout the room. Remember to equip Ebony & Ivory before you enter, since the bugs die in one hit. Even stepping on them is sufficient to kill them. Start stomping and blasting. Don't worry about killing every last one of them; there's more than 100 in the room. Just start near the door, kill the majority in one cluster, then move to the next, firing all the time. If you still can't do it, a Holy Water will clear the room in less than 1 second.
If you're strapped for Red Orbs, and you don't care about your Devil Hunter Rank at the end of the mission, you can farm this Secret Mission. Each Phantom Baby will drop 1 Red Orb, and you will get over 100 in the room with each attempt. There is no limit to the number of attempts you can make. Enter the room and kill slowly, making sure you run out of time before you reach 100 kills. Kill everything, collect the orbs, leave, then try again.