yeah I implemented being challenged from the practice mode after the release quickly. I felt the best way to avoid bugs was to reset the game. So in the end it does work, but it is a bit messy, sorry for that!
The bug where not all enemy units spawn is known and a total mystery for me. Whenever I try to replicate the situation everything works fine :( I will keep looking into it, but I don't have high hopes for finding a solution sadly.
The C + M debug trigger could really help in this case but only if you do it when the enemy units haven't spawned when they should've.