In general you are not moving around nearly as much indoors as outdoors. I do find that I get more discomfort on the trainer than outdoors, however you should not be getting numbness or pain. A couple things that I found to help was to stand up during the recoveries of the workout for 30 seconds to a minute or so.
Another thing you could try is some rocker plates so the bike has a bit of movement while your on the trainer.