Why are isomers difficult to separate?
Molecules which are made up of exactly the same elements but differ in atomic arrangement are called isomers. 

Since the two isomers have the same mass and charge, any seperation techniques which rely on a difference in mass and/or density would be very difficult.

Mass spectrometry is an analytical technique in which components of different mass are separated and detected, typically by ionizing (charging), accelerating through an electric field to a given velocity and finally, 'bending' through a magnetic field. The final position of the is detected as a function of its charge-to-mass ratio.

Any two isomers of $\small\ce{(C3H3)^+}$ have the same charge-to-mass ratio and therefore would be very difficult to separate and detect with mass spectrometry.