Based on the reference to E6, I'm assuming that these are slides, not negatives.
Are the slides mounted for projection, or unmounted?
If there is no sign of the white specs (dust?) on the slides themselves, then it sounds like the lab was just sloppy with their scanning.
I would tell them about your concerns. It is up to you to decide whether you should take up any offer they might make to fix the problem (re-scan?).
As for dealing with dust in scans, that's a bit outside APUG's restricted, no-digital mandate, but in my experiene, scans and the "clone" tool go hand in hand.