I had two water lines and a drain line sticking out of an upstairs wall, plumbing for a future wet bar. I decided to install the wet bar, shut off the main water valve, correctly installed two shut off valves, and nothing comes from the water lines once the main is turned back on. Is it possible there is a separate shut off main for these lines? I am confused.

Since the stubs where there before with not water coming out there must be another shut off somewhere. Your suspicion is correct, now you got to turn into a plumbing detective and trace the pipe back to the source

If the plumbing to the upstairs is being supplied from the basement/crawl area, as in new construction, these lines should have a shutoff valve at or near the area where they are routed up the wall or through a chase, should there be any problems-you could shut off those lines without shutting off the main. I would start by locating the supply lines in the basement, if there are no shutoffs at or near the area where they come through the floor, then you need to trace both lines all the way back to the original area where they were teed off. If you are built on a crawl, your floor should be insulated, which could make this a pain in he ***, since you will actually need to remove the insulation to make it possible to find any "hidden" valves.