This is Ben from Typekit. I just tested Futura PT Heavy in Illustrator (synced font) and in our Type Tester (web font). I've attached the screenshots below. In both, I'm seeing a standard question mark shape.
From the sounds of it, you may be using an alternate version of the "?" as an OpenType feature. You should be able to switch to the one you see in my screenshots. I'm happy to test this out, I just need to know which app you're using.
Sorry for the confusion here. I did some more research and it appears that this is how the "?" looks in the lighter variations of Futura PT. I checked the Paratype site (foundry that created Futura PT) and they show the same thing. For the lighter weights, the "?" has that upside down "S" look and for the heavier weights, it looks a bit more traditional.
Unfortunately, this isn't something we can fix since it's working as it should. There are some stylistic differences between the lighter/heavier weights.
Let me know if you have any further questions and we'll take it from there.