If you are planning on travelling for the interview in June, going back home and then arriving again in October - no, I do not think that having the Schengen visa will affect applying for the student visa.
In my experience, it is not difficult to get a student visa if you have been accepted into a course and have enough funds to support yourself. They will also understand that you have to attend the interview to be accepted for the course. Do you have a letter of invitation or anything that you can include in your application documents?
However, if you are planning on staying in Germany between your interview and starting your course, you will need to apply for an Aufenthaltserlaubnis.
This really depends on where you are from and what kind of agreements exist between your country and Germany.
My citizenship allows me to spend 90 days in the Schengen zone in a six month period, without needing to apply for any kind of visa.
A couple of years ago I arrived in Germany in mid-May and was to start my exchange semester in September or October, so I had to apply for an "Aufenthaltserlaubnis" (essentially, permission to stay in Germany but not to work) to bridge the period between my 3 months of stay in the Schengen zone and when my student visa would start. There were multiple bureaucratic hurdles and it was frustrating, but I did get the visa in the end.
My tips are the following, though they might not apply to you if you have to leave Germany to apply for your student visa (the possibility mentioned above):
contact your local German consulate or embassy and explain your situation and see what they say.
Make sure you have enough money saved to prove that you can support yourself. This will most likely be a certain amount per month, and probably also enough money for a return flight.
Check what kind of bank account you will need to put this money in. I had originally opened an account with Sparkasse, but the authority I had to apply for the visa through wanted me to open an account with Deutsche Bank.
Leave yourself plenty of time to deal with all the red tape and try not to get too stressed out if it is an annoying process. As long as you leave yourself enough time, you should be fine.
Good luck and viel Spass in Deutschland!