What in the world!? Smh. Wow, that should NOT have been ALLOWED to come back to you like that! (imo). Are you able to use your fingers to even test it to see if it could flattened out completely smooth all the way across the length of your bag? I'm hoping it's just wrinkles and not more like "pleats" due to the canvas not being completely aligned straight and FLAT when it was sewn! I know it's a hassle to return as you have to wait all over again but I personally would not accept that.
When I bought my Speedy Classic 25 it had some ugly folding marks. My SA told me they would fall out over time but I did not want to wait. I was able to get my wrinles out with a heated hand held hair dryer. What you can try for your issue is first completely stuff your bag as you need to have the wrinkles pushed out. Perhaps stuff it with towels, t shirts, etc. Lay the bag on the opposite side of the wrinkles and place a towel over the bag to cover that entire side of the bag that will be exposed to the heated hand held hair dryer. Heat the area with the hair dryer. After the area gets warm, turn off the dryer, remove the towel and start trying to smooth and massage the wrinkles out with your fingers and along the piping. You will need to do it while the canvas is still warm. You may need to repeat the process several times and you will need to make sure a towel is covering the entire side exposed to protect it from extreme heat. The canvas need to be warm when you try to smooth and massage the wrinkles out. Once it cools down, it won't work.
I've done this myself personally for my speedy to smooth the folding creases out. I actually did it without a towel and just held the hair dryer further away from my bag. I had to do it several times which looking back, probably took me a good hour. I finally got it to about 97% crease free and was happy with the results so I stopped. Over time by just using my Speedy and always having it properly stuffed when not using, it eventually smoothed out and now my Speedy is crease free. You can try this method but just be careful and don't rush through it. If you don't see any progress from doing it just a few times, I would just stop as more then likely, it will not smooth out and you don't want to "set" the wrinkles in place. If you can't just simply smooth it out with your fingers to see if it may smooth out (that its not sewn in that way) then using heat wont fix your issue as it was sewn in wrong to begin with. If you don't feel comfortable doing this then don't obviously. It worked for me but I understand most won't want to try it. I had a great result. The heat just softens the canvas to allow it to be somewhat manipulated but you need to allow it to get pretty warm in order to do this. You can also just see if the wrinkles fall out on its own but the way it looks, you may need to put in a structured base shaper or organizer and have it in there all the time to push those wrinkles out as it may never just "fall" out on its own. I'm sorry they sent the bag to you that way. Geez.

Perhaps just send the bag back to avoid all the hassel.