and basically I do not. I have realized that there are many many ways of doing projects and they all seem to come out fine when done. Many times a contractor will do some strange things in the process of building the project and when done it will look magnificient and work just fine. So to critique too early might just provoke him/her in a way that they might not take the care you want them to.
So, did you do your home work before hiring this contractor? Did you check references? Did you check the BBB? How much money did you pay up front for this job? How much do you owe upon completion?
The last think you want to do is to Bug him/her in the process of the job. A few spaced questions are fine, just to make sure your both on the same page, but to ask too many questions will drive me crazy and it has in the past.
I would want to know this: how deep is the regular slab? then how deep is the concrete area where he left the hole? Is the plumbing waste drain p trap and all waste water pipes set? Does he/she know that the floor of the shower will be level with the existing floor slab? He might be thinking that the shower stall pan will be lower than the existing bathroom floor. Did you let him know that that is NOT the case?
I would wait a few days and see what is the next step. Are there any other things that make you suspect other than this pan deal?