Continuity mistake: Just after the girls are quarantined, we see the ninja sneak into the little boy's room. He uses the sword to keep the door from closing, and some blood drips onto the floor. Two shots later, we see the same floor and the blood is gone.
Continuity mistake: When the ninja doll's eyes first open, they're blue. Toward the end, when he sneaks into Nathan's hospital room to stab him, his eyes are brown. (00:20:35 - 00:29:10)
Continuity mistake: When Phoebe first meets and talks to Nathan in the hospital, she has no ring on her right hand in shots showing her face, but in any shots from behind her she has a ring on. The ring appears and disappears between transitions during their conversation. (00:07:50)
Other mistake: When Prue astrals back to recite the spell to reverse the awakening spell, she and Phoebe don't actually complete the spell, they just recite the first paragraph "What was awakened for its sleep, must once again slumber deep" the rest according to the book of shadows is "return the disease to whence it came, so life can ease back to the same".
Answer: That was a mistake in the series.
Also, the episode is called 'Babies First Demon' and this alone tells us that it's Wyatt's first time in the field (so to speak) and as the sisters say, they've done a good job of clearing up their own magical messes so far. Nobody really knows how advanced Wyatt's powers are, or will become. That's why the cleaners appear, to nip things in the bud. The Cleaners didn't want to chance that the sisters could clean Wyatt's magic up, just incase they couldn't. Therefore intervening themselves, just in case.