You must have dynamic league evolution turned on. This will allow possible expansion and a lot of other changes, including, I believe, turning off interleague play.
If you start editing league structures and moving teams around, you're inviting problems. There isn't a feasible way to have have minor leagues evolve and change like they did in real life. The best bet is to have permanent affiliates at each level and not move them around or edit/delete teams or league structures. You can safely rename the minor league affiliates, but otherwise I'd advise against doing anything more drastic.
Also, what does the game status say. Does the indicator at the top of your screen say it's preseason? Or do you just think it's preseason?
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