Very messy LoR situation

[confusedaf]

So I'm kind of freaking out over my LoR situation. Applied for a Masters at my undergrad uni, and listed my dissertation supervisor as a referee. This person is really big in the field, was recently in the top 20 highest h-index scientists in the world. But since he's really busy, we have a day-to-day supervisor who manages all the daily work. I got the professor's recommendation as well as the daily supervisors and the daily supervisor uploaded a combined version. So question 1, is this against the rules technically if I am listing 1 referee but using 2 references in one? Theyre in a combined pdf, so will they just read the first one and ignore the 2nd or consider both? 

Second, on my application form, it shows the daily supervisor as the referee because they uploaded the reference - they're a PhD student (at the same uni). Will this look bad? I plan on asking the Professor to submit for all other applications. 

Thanks