2006 Prius Water pooled in right rear passenger floor board. No visible leaks.

I just purchased my daughter a used 2006 Prius and we found water in the rear right passenger floor board this morning. We have only had the car 3 days. There are on leaks that I could find inside the car. I looked in the tire well and water was there and also near the 12Volt battery also. The brownish/yellow sealant in the tire well that goes around the bottom is also in my 2010 Prius but I noticed that my daughters 2006 Prius the sealant or what I believe to be bodyflex is cracked. I am going to have a body person look and see if he agrees with me that this bodyflex is cracked. Has anyone else had this problem.