Standard international tickets are valid for 30 days, so you can get off at any stop you want on the route.....but they are a lot more expensive, they are available on the day at the station, no need to buy in advance or on line.
If you really want to stop in Bratislava, buy Prague to Bratislava ticket on line from Czech railways eshop for circa 16 euros, and buy additional ticket from Bratislava to Budapest in person in Bratislava. Used to be that if you buy a return ticket,(B'lava to Budapest) it is cheaper than a single one (16 euros) but no idea if that's still the case. Ask on Bratislava forum....
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