PhD admissions: Overlap between B.Sc. and M.Sc. transcripts As I wrote in my previous question, I am currently applying to PhD departments in the US (from a German institution). Beyond the language problem, there is another aspect that worries me: 

I finished my degree back in March 2015 and then decided to fill the time from then to Fall 2016 (start of PhD programs in the US) by starting a 2 year M.Sc. in the same subject, which I planned to finish in 1.5 years (and will also manage to do so). 

Officially I enrolled in that degree this September. Nevertheless, I "unofficially" started with the degree already during April 2015, by staying enrolled as an undergraduate and taking "additional courses" (i.e. graded courses beyond the required number of credits, which also do not influence the final grade). Since the Master and Bachelor degree were offered from the same university, they then simply approved all those additional credits as part of my MSc degree.

Now, my problem is that these courses are mentioned twice in my transcripts, once as additional courses of my Bachelor's degree and once for my Master's degree transcript. Do you think this could confuse the admissions committee? Should I maybe refrain from submitting the M.Sc. transcript since officially I am enrolled only from the Fall semester and the universities do not require transcripts from the Fall semester? Also note that currently the M.Sc. transcript does not contain any information about courses not included in my B.Sc. transcript. Or should I try to mention this somewhere (I am particularly worried about some universities which do not provide any opportunity to leave such comments/remarks).
Your two degrees sound reminiscent of the "3-2 combined" programs that are common in the U.S.  Read up on a couple of those and I think you'll start to relax.

Please do let the admissions committee know what you're doing this year.  Perhaps that information can be fit into one of the standard documents -- perhaps your CV, perhaps a cover letter or the statement of purpose.

No matter how streamlined an online application process is, I would think you could contact the department and ask them what email address to use for submitting an additional document that didn't fit into any of the pigeonholes provided.