There are many problems with the storyline of Jenna putting "something" in the toilet without telling Jerry:
1) When Jerry helps Kramer take the road signs back to his apartment, Jenna shuts the door so doesn't know what she put in the toilet. However, there is only about a 5 second difference from when she shuts the door and opens it again. Therefore, it doesn't seem likely she would have the time to put something in the toilet and then quickly open the door again as if everything was normal.
2) If she did do it that quickly, its definitely impossible that she would of had the time to take something so big and so far away such as the SOFA CUSHION, put it in the toilet, put back and open the door within 5 seconds!
3) Wouldn't Jerry notice that something was notably wet when put back to its normal place?
4) There are many certain things in Jerry's apartment that Jerry threw out that would either not fit in the toilet, or were too far away and things that Jenna wouldn't have had time to put in the toilet, such as the couch cushions or the dishes. Jerry should have known better.