If the phase pods allowed them to run through walls, etc., then why didn't they fall through the floor?
Regarding transporter knowledge and/or use, it's reasonable to assume transporters used by certain categories of people (e.g. military vs civilian) would have various default settings. For example, civilian transporters might have a default setting to exclude weapons transport. All transporters might default to exclude known parasites, foreign organisms, and so on. So, even if one didn't know how to operate a device, its "safeties" would likely prevent major functional screw-ups and protocol errors.
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