Everything has a weakpoint...
The Bijuudama is a mixed concentration of red and blue chakra. Additionally, as seen by Killer Bee's initial one, and the fact Rasengan is based on it, the bomb is actually a spiraling mass of chakra.
This provides two attemptable counters.
A) Disrupt the rotation of the chakra.... by doing so, the chakra would thusly either spiral out of control (pre-detonation), or it would disperse as with the core rotation gone, the chakra is simply flung in multiple directions.
Such a feat could feasibly be done via the Enton Arrow (though it may need to be a Perfect Susanoo Enton Arrow). By firing to disrupt the core, or by aiming to hit the perimeter/circumference of the circular object... it would be possible to do so.
B) Disrupt the Balance of Red and Blue chakra.... Bee mentioned that it requires a perfect balance to maintain, and Naruto was seen failing his Rasengan variant because he had an incorrect concentration. Through possibly Enton's (Amaterasu) ability to burn what it targets... it is theoretically possible to disrupt the balance... it would not perfectly counter it since the detonation of failure would occur; however, it would instantly stop it from advancing.