Question

why does a fly experience greater acceleration when it collids with a fast moving bus

Answer 1

Newton's Third law
action equal in magnitude and opposite in direction to reaction
so if force on the fly is F that on the bus is -F.
Second Law
F = m a
m fly a fly = m bus a bus
so
a fly = a bus (m bus/m fly)

Answer 2

the fly's mass (relative to the bus) means that the momentum of the fly is essentially incorporated into the momentum of the bus

depending on the relative velocities, this can mean a massive acceleration for the fly
... more than the fly's structure can tolerate (squish)