For the Be Scanned issue: It occurred when my Sim was on a community lot trying to Experiment with Zero-G, every time he was doing it, a Plumbot tries to scan my Sim causing the action to be canceled. Even when I cancel Be Scanned, he still exits the building.
For the soil rug: I was using a large room for gardening in the basement which is enough to store mainly every plant. Even purchasing a new sprinkler doesn't fix the affected plants but moving the plant outside near a sprinkler in my original garden or in the rain waters it. I haven't tested if the affected plants (I haven't planeted one so far) get watered in the rain on the soil rug because I do know the rain from Seasons affect planter bowls correctly while many plants on a planter bowl still need watering even under a sprinkler.
I believe the planter bowl issue first occurred in Supernatural and still occurred in 1.57 when I have used the planter bowls. I haven't tested the planter bowls in Into the Future.
In addition, the no click on Sim bug also occurs in Oasis Landing, not just Sims University.
I think I know why it rains on Bolts Emporium, Cafeteria, XI Import Gallery and the Future Lounge is because the outside building is actually an object which is the building's shell, not a wall, floor tile and roof. I've seen the objects using Buydebug and noticed the shell for the community lots. Also, it appears that EA did not put a floor tile for its roof. If a lot did not have a floor tile on the top floor or roof, it would rain and snow on the lot similar to the 4 mentioned lots. Rain also goes through buildings too such as the theatre in Monnlight Falls, my Sim got soaked when when under the theatre's roof but it did not occur when he was in the theatre.