I have a rattling noise when engaging first gear and taking off from a stop. It's annoying and probably more annoying for the dealer who I must go ask to find the weird noise. I worked at a dealership in the 90's. Techs hate warranty rattles because the manufacturer doesn't pay squat to check out rattles and the tech normally says that they can't duplicate the problem. This manual trans is no match for the silky smooth Honda manual transmission from the late 80's to mid 90's. Those were like butter. Nothing better was on the market. This manual trans is good, it just isn't as excellent as Honda produced in the past.

 

you didn't say if the bucking also happened with engaging first gear so I presume it doesn't; at least you notice.
We think the problem is a hard take up of the clutch plate to the driven plate that's a function of the clutch material surface or clutch springs. It can be a defective clutch plate material that shows up as rough shifting prior to you and was the result of the prior owner/driver.
try taking up the clutch in first and in second very gingerly and slowly so any bucking (sudden engagement of the clutch) is least likely. if it does anyway, suspect the clutch material or weak spring(s) and you can check with the dealer who sold you a car with defect if you can but the likelihood its now your problem and only a new clutch will suffice. yes its possible the clutch surface could be refinished but that's a long and potentially expensive route. just replace the clutch and check the shifter etc.
good luck.
ps if the slow takeup doesn't result in bucking you may just shift slower and easier til it wears in OR if it doesn't wear in the springs may be the cause and clutch replacement is your only solution. sorry.

 

I am not sure of what oil they use from the factory but consider using 100 synthetic such as Red Line.

 

Be careful to get the right Redline. I put their recommended oil in the tranny of my 1990 Toyota truck and totally lost the synchronizers. One of their engineers sent me a bottle of friction modifier to add and it restored them.

 

Yeah, customer service my ass. Honda has had a social media damage control person on here since the 3rd rate rollout of the 3rd gen Fit. All you're going to get at the dealer is the standard "operating as designed", "cannot duplicate at this time", "no trouble found" BS, and all it will cost you is a day you could have better utilized more productively doing almost anything else. The Mexico plant is big stakes for Honda, hence the forum mouthpiece.