What is the Hiraishin no Jutsu's weakness?
Over-reliance and Predictability  


If the opponent knows that Hiraishin no Jutsu allows the user to teleport to marked kunai and area, it would be "easily" countered.  


Minato vs Raikage: if Raikage also knew that Minato left his mark on Bee, he (Raikage) could instantly move to Bee (at this point Raikage already spotted almost all of Minato's kunai) and Minato would probably moved to other kunai and Raikage would chase him again (I don't know what the final outcome would be, though)
Tobirama vs Madara: Madara immediately countered Tobirama the moment he used Hiraishingiri because Madara had seen that move before


Of course this can happen (Hiraishin being countered) only if the user of this jutsu rely on it too much and can't finish his/her opponent immediately.

Edit: oh and also if the opponent is fast physically or reactively

Edit 2: Madara sensed Tobirama with Sage Mode, then he's fast enough to dodge it.