I believe you've actually answered your question in the question itself.
Wormtail and Crouch Jr did not capture Moody without any noise. You write:
We journeyed to his house. Moody put up a struggle. There was a commotion.... I was ready to face Arthur Weasley when he arrived to sort out the Muggles who had heard a disturbance.
This quite clearly indicates to me that the Muggles were indeed alerted by the noise and commotion of Wormtail and Crouch Jr overpowering Moody. Here's the full text in question, though:
‘Wormtail and I did it. We had prepared the Polyjuice Potion beforehand. We journeyed to his house. Moody put up a struggle. There was a commotion. We managed to subdue him just
in time. Forced him into a compartment of his own magical trunk. Took some of his hair and added it to the Potion. I drank it, I became Moody’s double. I took his leg and his eye. I
was ready to face Arthur Weasley when he arrived to sort out the Muggles who had heard a disturbance. I made the dustbins move around the yard. I told Arthur Weasley I had heard
intruders in my yard, who had set the dustbins off.
Goblet of Fire - page 598 - UK Hardcover - chapter 35, Veritaserum
The dustbins were a secondary disturbance and a distraction, as I read it. My interpretation of the passage would have Crouch Jr setting off the dustbins to cover up the disturbance caused by Moody's abduction, so that when Arthur Weasley (Misuse of Muggle Artifacts employee) came around, Arthur would chalk up the commotion to the dustbins and Moody's propensity for paranoia and CONSTANT VIGILANCE (!). Crouch Jr hoped Arthur would not investigate the matter thoroughly. Sidenote: it is actually Amos Diggory who later first questions the events of the night of Moody's capture.
I don't think you're missing anything, to be honest.