My car only has 30,000 miles on it. I think I use the clutch properly and don’t rest on it or anything. I have driven a manual transmission for 35 years. After 2 years, my civic started to shudder a little going into first and second (just a touch into third). However, it will happen for a day or 2, and then be fine for a week, and so on. The honda mechanic test drove with me and heard it “every time” but they could not repair it then. When I took it in, it was not doing it. I can never get it to the dealership when it’s happening. I’ve tried the start it moving in 5th and it kills, so that means the clutch is good I guess.
Civic 2003 here - my clutch worked fine until about 95K miles, then started with the symptoms you describe.
I was worried I might need a new clutch, but then tried some tough love with it. The problem you are experiencing can very likely be a glazed spot on the flywheel or a spot of uneven wear on the clutch disc. It can also be a busted motor mount or a couple other things, so get those checked out if you haven’t already.
My fix:
I took the car out onto an open stretch of highway and got it up to 80 (Flow of traffic - this is california). I then kept my foot on the gas and pushed the clutch in about halfway, just until it started slipping for 1-2 seconds. I did that about 2 times to “burn” the clutch just for a very, very short duration.
After getting off the freeway, my chatter was gone. Hasn’t come back yet in about 2 weeks. YMMV, and if this does not fix the problem, definitely have it looked at. It is possible you have a clutch fluid or rear main seal leak in your engine and the fluid is causing the clutch to slip. Check the level of fluid in the clutch reservoir.