It might be as simple as this:
If you share a sample here of the f3d file, a number of people would be willing to help figure out what is happening. If it is something that you would rather not share, mock up an example that is having the same issue. If you follow the link above, the OP was having a new problem and it turned out that during ‘manufacturing’ the X-Z plane was picked when the sketch and body were both in the X-Y plane.
I do agree that for us occasional users, the changes will slip is up. I will also say, with each change Fusion 360 has made, once I finally caught on to how it worked, it turned out to be a ‘helpful’ change.