I've also had the pet store disappear after being placed. Everything on the lot was just gone. Sort of.
I thought I had just forgot to place it so I went into edit town to do so, only to find I couldn't place the lot where it was slated to go. The lot just appeared to be gone, so I decided to place another with the World Editor...only to find out that there was something there. I finally decided to just remove the empty lot that was there so I could replace the lot, and when I clicked the sledgehammer tool, an icon finally popped up where the lot should have been, but wasn't (but apparently was). Clicking on this seemingly empty lot demolished an invisible building, and after that I was able to place the pet shot.
Strange, really...