^ Yeah, I really think (from what you say) they made the wrong decision, there.
I understand that the bag wasn't damaged/faulty when it, originally, left their store.
But, from what you say, it (very quickly) ended up that way, due to their actions; not yours.
If the bag had been six months old and/or well used, when all this happened, then to only offer a further free repair would be fair enough, I guess.
But, if you only used it once, then it's not OK.
You shouldn't (and don't) have to use a bag the day you get it to ensure you will be covered, if anything goes wrong.
It is perfectly reasonable to buy an item and then not use it for a few weeks.
If they suspected you had used the bag more than once (or a few times), then that would be a different matter, as it would no longer be a nearly new bag.
So, at that point, expecting them to replace an old bag with a new (or refund) would be unreasonable.
But, if not, their decision was unfair.
In future, they should probably consider telling their SAs to say nothing re. bag care and just refer customers to the care cards; rather than risk them giving out misinformation.
That way, any colour transfer would definitely have been your responsibility.
Even if they would still have been responsible for any (further) damage the repairers caused.
They should also have a word with their repairers re. taking care not to do further damage to items and safe packaging methods.