Again, it was a defective lens that after it left the factory had an issue and returned for repair. It could have been a very minor thing or major. If it were a camera it could have been a firmware change, but not as likely with a lens.
Most companies would sell these as factory seconds, Canon chooses to sell them as new. If this bothers you and you bought it from someone like B&H the will exchange it with no fuss. There is a chance that some idiot retailer is marking new clean boxes. Rotating inventory to keep it fresh. I guess they think lenses are like milk and will spoil.
Let me modify this a bit, it could have been a missing or broken item like a bag or cap, it may have not been the lens at all.
Whilst I agree with your opinion, the wording seems ambiguous, Canon do not resell items that have been returned from retail customers as new, if it were Canon USA would be open to all kinds of legal issues.
If it is a Canon affixed blue dot I believe, and this is certainly true of Canon products in the past, that there was a factory recall of all inventory between certain serial numbers that had been sent to importers and retailers, so the items are still considered new, unsold and unused. To keep track of which stock have had checks or adjustments made a blue dot is affixed, after blue dots if there is a second reason to recall then they have affixed yellow dots. I further believe that the reasons are often because quality control throws up question marks on component batches.
But this is not definitive and could also be used as internal stock checking or any number of other reasons for easy visual checking. I have personally seen, blue, yellow, green and red dots on new Canon boxes, both bodies and lenses.