Alright, seems like we figured out the root cause of the above errors: it turns out that if you copy the windows (sub-surfaces) into other levels, such errors arise. If at all, one wants to copy/duplicate levels to save time. Following workflow shall be followed (based on my experience):

1. Just select the level(s) you want to copy (there shall be no windows or any sub-surfaces in such levels).
2. Select the "Move" command from palette and press "Ctrl" key from keyboard to duplicate/replicate/copy levels.
3. After you are done with copying the selected levels, you are safe to add sub-surfaces to the building envelope.
4. Here, I would also add that, always run the "Surface Matching" script before adding the sub-surfaces (windows etc.)

Few tips: Keep saving your .osm model at each step and consistently check the warning/error log (the orange triangle with exclamation mark), to make sure its going well or not - that way you can always go to the previously saved .osm file, in case the current one comes up with errors.

I would like to extend my gratitude and thanks to Denis and Jamie, whose answers (above) undoubtedly were helpful and a guiding source. Much appreciated guys!

PS: Anyone, please upvote if you find this helpful. Cheers!