Got a response from EYW today. Looks like they'll resolve the issue for all affected in February.
Firstly, we would like to thank you for your patience with this matter.
Upon inspection of your bookings and the Speedbump challenges, we noticed that our system was excluding some bookings made on Nov.14 & registering them as made on the 15th. This is due to the the fact that booking times register in Aeroplan's system in Greenwich Mean Time. Based on this we have concluded that anyone who booked a flight for the 1st Speedbump challenge up until 02:59 EST on Nov 15 (07:59 GMT) would be eligible for the miles associated to the 1st Speedbump challenge of 1,000 Aeroplan Miles per segment booked. The same logic would apply for the 2nd Speedbump challenge, anyone who booked up until 02:59 EST on Nov 18 (GMT) would be eligible for the miles associated to that 2nd Speedbump challenge of 1,000 Aeroplan Miles for every round-trip or 2 one-way segment booked.
We are currently running a query to see how many customers/players were indeed affected and then find a fix to credit everyone accordingly. This will require both our systems and Aeroplan’s systems so it will take some time - roughly 2 weeks in order for the correct amounts to show up on you Earn Your Wings Profile and Aeroplan account.