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Re: 2010 Civic Si
The problem is likely in the master cylinder or the pedal itself. There are very likely plastic bushings where the pedal arm rides on a shaft. Those could be worn, allowing the pedal to move a little bit in other ways than just being pressed. That could make for clicks, but you should feel that through your foot.
Could be the clutch master cylinder, assuming an hydraulic clutch. (Early Civics were not, later ones were.) Could also be the slave cylinder (at the transmission end) or the throwout bearing or pressure plate. The latter two mean a clutch replacement, more or less. You don't have to replace the clutch to fix those, but since you have the transmission out it makes sense to.
I personally wouldn't worry about it unless you have a warranty that will handle the repairs for you, or unless it gets noticeably worse.
-soD
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