I've had this problem on/off since about ~20k mi and it has gotten progressively worse. Basically, I believe my TCC has issues...specifically the lockup and/or the controlling solenoid. Gentle acceleration causes the lockup to 'grind' or make a shudder sound (similar to a missed shift on a MT). Two different Honda dealerships 'Can't replicate problem' so they claim is doesn't exist despite me having a recording of it ( ). I'm close to 57k mi now and I want to identify/resolve issue while it's still under warranty. My biggest fear is that all these miles with this issue may be causing more long term damage than is apparent. Probably the first and last Honda I'm ever going to buy.

 

I say leave it with them for a day if they can't replicate the grinding in one afternoon. Most dealerships tend to go that route if they couldn't replicate the problem in the first place.

 

I believe this is the same sound I experienced (and others have). Listened to your youtube and this seems to confirm (although my Fit doesn't sound that rumbly )

Gentle acceleration, perhaps up a slight incline. shift from 2nd to 3rd. Happens more often when the engine cold light has just gone off but it's not really up to operating temperature.

Under these conditions there was a noise I would characterize more as fluid rushing from a high pressure area to a low pressure area through a narrow orifice.

Changing transmission fluid (simple drain fill of about 4 quarts) to the newer Honda DW-1 fluid and it went away.

Started around 20K miles. Changed at 30k. Haven't heard it since.

I don't think it's a problem either way, but I prefer not to hear it.

Here's an older thread on the topic.

 

Hi There,

FYI - I looked at your YouTube, and can confirm having the exact same noise in my 2010 Fit Sport (noice occurred in my automatic transmission Fit when it shifts from 2nd to 3rd gear and moving at a normal pace) Problem started at about 15,000 miles.
It took me 2 years and multiple visits to convince Honda Dealer that the noise was present, and that there was a problem that needed to be addressed. I'm happy to report that they finally listened to me, just before my power train warranty expired. They replaced the Torque Converter under warranty, and problem was completely resolved. My fit is as good as new!

 

Wish i knew this. My Fit has made this noise for 94,000 miles...since 1st drive off the lo with 4 miles on odometer. I complained at everyone of my service visits until warranty was up at 80k.

 

I have a 2009 Fit 5AT which had the EXACT same noise during some low speed shifts. It would not always do it, but it greatly concerned me as well. What took care of the problem was simply to do a complete drain/fill of ATF. It's as easy as changing your own oil. Noise goes away completely after you're done. I found no particles or problems when draining the old ATF. You need to only drain/fill 1x every 30,000 miles or so to maintain it. The refill is 3 qts, BUT to get a complete change you need to to drain/fill 4x, so you'll need 12 qts. Just get a case of Honda ATF. I found the best price from Bill Kay Honda, $99.61 shipped for 12 qts.
08200-9001 | FLUID (ATF-Z1) | Honda Replacement Part

 

They assigned me a repair guy that took the car out (with me in the passenger seat) and listened very carefully for the noise (same one you demoed in your YT) The repair guy actually did hear it too, and suggested it might be the torque converter. They obviously could not do that kind of repair without proof, and they did end up finding filings pieces in the transmission fluid, and took the torque converter out and photographed damage to it to send to Honda for free replacement part.
They also carefully examined all other transmission components for other damage, but found nothing else wrong. Honda replaced the TC one month before drive train warranty expiry. (A rather expensive repair FOC). The guy told me that Honda will also sometimes do an after warranty expiry repair if problem was noted by you in multiple service checkups history, and they can prove the problem still exists. I guess it really pays off to get lucky enough to have honest dealer repair service.