I wonder how they prevent contamination of the containers used to collect and store samples.

I assume they have to be ultra clean in every sense of the word 'clean' with the cavity pulled to a vacuum. And also the equipment that collects the sample and puts it into the canister has to be clean as well.

The logistics aren't obvious to me at all

They seem pretty confident. There's been some conflicting reporting on contamination of the Ryugu samples over time.

https://phys.org/news/2024-11-ryugu-asteroid-sample-rapidly-...

> Researchers from Imperial College London have discovered that a space-returned sample from asteroid Ryugu was rapidly colonized by terrestrial microorganisms, even under stringent contamination control measures.

https://www.isas.jaxa.jp/en/topics/003899.html

> As described in the discussion of the journal paper, all samples received from JAXA have undergone the initial description, storage, and sealing in dedicated containers under a nitrogen atmosphere. The samples are distributed to researchers without exposure to the Earth's atmosphere. The possibility of microbial contamination is therefore considered extremely low. In addition, organic and microbial contamination assessment of the environment at the curation facilities within JAXA (clean chamber) in which the Ryugu sample grains undergo the initial description are conducted 1 ~ 2 times a year. It has been confirmed and reported that the concentration of organic matter is at or below the same level as that of the OSIRIS-REx asteroid return sample glove box at the NASA Johnson Space Center, and that no microbial colonies have been detected in the microbial contamination assessment conducted with swabbing and culture medium (Yada et al., 2023). Based on these facts, we agree that the microbial contamination described in the paper did not occur during a process within JAXA, but under the laboratory environment of the allocated researchers.

https://science.gsfc.nasa.gov/sed/content/uploadFiles/public...