On the OEM 06-11 Honda Civic clutch master cylinder there is an offset chamber that the fluid travels through to get your foot motion to transfer to the clutch. This chamber actually causes the fluid to slow, resulting in a clutch that does not disengage or engage fast enough. Which leads to an inconsistent foot-shift movement and in some cases transmission grinds. It's not your fault!
The simple solution is to upgrade to the older generation Honda Civic master cylinder and included braided stainless line. Problem solved. The new master cylinder also has steel internals while the OEM unit has plastic internals.
You will need to swap out the OEM rod & clevis
02-06 Acura RSX (other adjustments to the pedal may be required)
06-11 Honda Civic Si
12-15 Honda Civic Si (other adjustments to the pedal may be required)