There are plastic cupcake holders that keep them in place while in the box. (Not exactly sure what they are called) They resemble a cupcake pan only they are shallow.
I used to buy those, too, until my cake supply store started selling clear plastic cupcake "carry-out" boxes...like a take-out box from a restaurant, but make for cupcakes, and they were cheaper than buying the cupcake insert AND the box, but 25 cupcakes is an odd #....I would suggest eating one and then you will have a perfect fit 
Or you will have to buy an extra cupcake holder for just one cupcake OR make 11 more cupcakes as a bonus.
I've recently did a cupcake wedding of 85. I put the cupcakes in the window boxes into the bottom of which I had placed two cake boards (for stability). The boxes with the cake boards held the cupcakes nicely.
hi there, ive just started doing cuppies for bridal showers, my 1st order was for 160, so i went and bought the biggest cakeboxes i could find, then i went to my local $$store and bought the aluminum cupcake pans, i poked a finger sized hold underneath each cc space, i slid the cuppies in, put those in the covered cake boxes and off i went with out a single casualty!! lol, then when i set up, all i did was poke my finder throught the hole underneath, and i took the cc out with out ruining the icing.
What I do is buy a t-shirt gift box (2 for $2 with lids at Walmart) put a piece of cardboard covered in tin foil then put the cupcakes in with mini marshmallows spread around so they don't move, it should fit 24-25 depending on how you manouver them in there. here is a link to a forum post along with a picture i posted. HTH
http://www.cakecentral.com/modules.php?name=Forums&file=viewtopic&t=632129&postdays=0&postorder=asc&&start=15
I use either those white plastic shallow thingies in a box OR the clear plastic carry-out looking containers.
As for 25 cupcakes. . .PITA. . .I only sell cupcakes by the dozen, minimum of 2 doz. It is ridiculous for you to waste batter because someone wants 1 more cupcake. They need to decide if they want one less, hoping someone won't want one OR if they want some delicious little treats to have later. And don't give them away as a bonus. . .they gotta pay for each one.
You can always freeze any leftovers for an inpromptu tasting.
The mini marshmallow is nice but if your trying to make a profit that will eat it away. I just use icing underneath and have not problem besides using a boxes designed for cupcakes.
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