Mystery of a Thousand Moons - S1-E18
Continuity mistake: In the previous episode, the Republic troops blasted huge holes into the Separatist lab to enter it. In this episode, in which the highly contagious airborne virus is unleashed into the facility, the holes are conveniently nowhere to be seen, so it can't get loose onto Naboo.
Answer: I guess that 1) the King assumed that Ventress' droids were meant to capture the Jedi, not kill him outright. When she yells at OOM-224 to shoot Yoda, she evidently failed that expectation. 2) Sending out a bunch of Droidekas after it is plain that Master Yoda has clearly won is not a sign of good sportsmanship, either.