Well, what happened in real life is that the bridge set was set up for filming "The Cage," stored while the network was making up it's mind, reassembled (differently) for the filming of the second pilot and then broken down again and moved to the studio where the production would actually be made (a totally different stage area (Actually a whole different lot IIRC, but I might be wrong)) and reassembled for the final time, this time in a third configuration that stayed more or less the same for all three production seasons. So it wasn't just a screw up of the wild sections. As far as I know, they were always placed in the right order throughout the show. If that's not true and someone has an example of a section is the wrong place I'd like to see it, but I'm not aware of anything like that.
I do find myself looking as the middle row of blinking lights a lot during shots on the bridge and at least Spock's, Uhura's and Scotty's stations are always in the right spots. I know because I recognize the displays, I'm not as familiar with the other ones, though.