In the Barbell Training jpurney sometimes I did a run before a leg day. Then I adapt my session and exclude the legs, but why freeletics is changing it to a only body workout??
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Hey Tristan 
This is simply the way this Journey is designed-the adapt options will vary from TJ to TJ.
You might have more flexibility by simply completing a different session from your upcoming week. Of course this assumes that there is a more suitable session scheduled 
I’ve got the same issue as Tristan. And not just once, but every single time. I do other sports as well and they usually involve my legs quite a bit more, so on some days I’d like to do the upper body and core bits of my current TJ (Dumbbell Gain). But whenever I try to do so, it changes the entire workout to core only.