Transmission/clutch makes "jar of marbles" sound when engine braking in 1st-3rd gears
 

This is for manual transmission during deceleration.
I notice there is a "jar of marbles" sound during engine braking (deceleration).
It starts at about 2200 RPM and ends at about 1200 RPM.
It makes the noise only in 1st, 2nd, and 3rd gears. Not in 4th and above.
Does anyone else notice this noise?

I forgot to mention one thing. I have a manual transmission.

But no one else hear this noise? I'm starting to be worried if my car is the only car that makes this noise. :(

In my honest opinion it may just be more vibrations due to the engine stressing at low rpm with gear load; I suggest clutch in at 2k rpm or downshift if you have to speed up again.
I downshift naturally any time I slow down, but it just feels unnatural & harsh to let my rpm dip below 2k; when not spirited driving (or racing) I actually only downshift to as far down as 3rd then clutch in at 2k RPM; not trying to mash synchros, I do not go down to second when doing normal street slowdowns becuase the 2nd gear synchros seem stressed if not downshifting from a higher range RPM

Maybe it's the transmission rather than the engine, because automatic transmissions run the engine all the way down to 1200rpm or lower before downshifting and no one really talks about them having the vibration issues (locked up).

I havent ever noticed that, but I will keep an ear open tonight. Are you using engine braking only, or engine braking AND foot brake when you hear it?

I'm using engine braking only. If I use foot brake too, then the RPM would go down too fast to hear this noise. It's hardly noticeable in 1st or 3rd gear. 2nd is the best gear to hear this noise. I don't hear it on 4th to 6th gear. The windows need to be closed, otherwise the engine noise coming from outside is louder than this noise, so you won't hear it. It's loudest at around 1600 RPM.

That makes sense. But the thing is, all the Toyota cars that I had didn't make this noise. I usually don't step on the clutch during engine braking until 1000 RPM and I've been doing that for 7 years. Maybe this noise is a Subaru thing and is normal, but I'm just curious if anyone else is hearing this noise too.

It's very possible it's just a heat shield. Check the heat shields around the engine and exhaust. Or even easier, just bring it to a dealership, It's not going to cost you anything but maybe 30 mins of your time and they will be able to have someone looking for the noise under the car while it is running since it will be on a lift.

I noticed that the sound tube resonator box can easily rattle against the intake manifold.

It has soft rubber mounting.

Since it only happens when it's in 1st, 2nd, or 3rd gear, I'm wondering if this noise has something to do with the triple cone synchro.

Anyone notice this noise yet?

Yeah we had a discussion going on in the new manual drivers Q & A about this noise.

Yep, I was part of that discussion too. I'm wondering if anyone else is experiencing this noise during deceleration (not acceleration).

I've heard the noise. I've been able to get it to occur when being feathery in the throttle at low speeds in first/second gear (say below 2k rpm). I'm used to riding second gear sort of low (6-10mph) while in parking lots looking for a spot. When I give it a little gas, I typically hear that noise. Pretty sure it normal.