Hi Gregor - OK. It took me some time to see exactly what is going on here. I cannot say for certain if this is indeed a bug - but the behavior of the software is difficult to follow. I will check it with some of the development teams.
However - it is not really difficult to see why there may be undesirable behavior from the software, as the structure of your design is not ideal.
The root of the issue is that you have created two components: "Component 1" and also "Mid". The outer edge of the box has NOT been defined as a component.....this is simply a Body - under the name "Base". In the first pattern of your cut - the cutting is occurring in both the component "Component" and also in the body "base". Once you switch to the variant with the component "Mid" - the same cut is trying to cut two components, namely "component" and "mid".....I am not sure if the software is SUPPOSED to do this, or not....there may be a limitation - or perhaps I am forgetting something. In any case - I can certainly understand how a user would be confused by this. I will discuss it - as already stated.
I would, however, make another suggestion, which I believe will result in 1) solving your problem 2) better, more reproducible results for all cases in the future.
Is there a particular reason this assembly structure was chosen? I cannot see an obvious reason to create the base body as a body in Fusion, while creating the two other bodies as separate components. Additionally - the two components have been defined by creating sketches which are embedded in the components themselves, and not at the top-level of the assembly.
The structure effectively creates sketches which are defined in one component, and uses these to define features in another component. In most other CAD systems, this would not be possible at all without the use of an assembly feature - and even then - these are notoriously unstable and very bad for performance. In truth - it looks like we don't handle it all that well either in this case.
I would suggest instead to either choose a top-down design structure (clearly the better choice in this case) or a bottom-up structure and remain consistent in their use, instead of doing both - as was the case here. It is much more likely to cause trouble for the software - but also - and this is even more important, it will be very difficult to follow your design. Changes will be difficult, and reuse will be impossible. In effect you get the worst drawbacks of both philosophies - with none of the advantages.
Here is a link to my Version for you: https://a360.co/2OxtbcC
and here is a link to a YouTube video I made on top-down design: https://youtu.be/L9Evb3ZxD40
and here is a link to a video where I discuss your file and the version I made: https://www.youtube.com/watch?v=hdIWHIMtbiw
I hope it helps you. I will respond again after speaking to development.
Mickey Wakefield
Fusion 360 Community Manager