if you're making it an 'independent' league (rather than a 'major' league), the game is probably setting the average attendance low, so the ballparks are being structured around that expected number....
just created an independent league to check it.... the financials tab had the expected attendance at 2000, and the majority of the ballparks had capacities around that (though one snuck in with 48000
)....
went to create the same league setup only as a 'major' league, and the expected attendance was 50000; and all the teams had parks with capacities at/over that number...
so I'd say check that field in the initial setup and set it to what you want... might have to edit a couple parks that sneak through that don't fit the theme but that's easier than having to edit them all