The Intercity bus from Munich to Prague STARTS at 29€. (19€ is for the bus from Nürnberg to Prag.) The ticket is a Savings Fare - bus specific - good only on one bus (time) on one day. It is refundable less a penalty before the day of travel, non-refundable on the day of travel.
If you purchase a Bayern-Boehmen-Ticket (26€ plus 4,50€ for travelers 2-5), you can travel on those trains (there are two per day, direct (9:01 & 17:01), plus one at 12:44 with a dedicated change in Schwandorf) to Pilsen where you can purchase a Czech Rail ticket to Prague for 100 Kc (about 3,65€). The Bayern-Boehmen-Ticket is always available up to travel time for that price and is valid from anywhere in Bavaria to Pilsen.
So, 29,65 for one person on the train, 18,90 each for 2 people on the train, from 29€ for the bus. If you just go up to the window (or bus driver), Joan, the fare to Prague from Munich by train is 69,10€ or by bus (if still available), 66,20€. There is a significant "tax" for not planning.
Update: I see the Bahn has changed the schedule. Now, all three ALX rail connections to Prague are direct. The trains stop in Schwandorf to pick up passengers from a train from Nürnburg.