I didn't think anything when Fiona slept in her water bowl until I took her in and she was real sick. Now watching Shrek and his two new friends I notice the water bowl is only a stepping stone to the rest of the tank. I never see them in it, unless they are sticking their butt in it!

Go with your gut, if you think their is something wrong take him to the vet. It's better to be safe than sorry and if the store is going to pay for the visit, that's more of a reason to do so!