Hello,
The workflow log shows "the truth", that second decision step may have come from a different workflow instance or you could be interpreting it wrong.
Is that screenshot the chronological view? You should use it, it makes it very clear what is going on.
You say that the Set Container step isn't done but how do you know this? Is it set to be shown in the workflow log?
" But in a loop step, the sub workflow gets completed but control comes to the first step of the main workflow instead of the next step of the step type in which the sub workflow is used. "
The first is impossible and the second does not make any sense. Step of a step type?
Trust the workflow log!
regards
Rick