I just have graduated university and currently am applying for a master degree and various positions on different labs as I am eager to go deeper into science. I have been asked for two references together with other documents. As I had two different internships I have asked my former supervisors to write me a recommendation later, one of them wrote me a very good reference but my bachelor thesis supervisor besides explaining what experience I have gained in a lab wrote not a very positive reference stating that the analysis of data I have done were hard to understand and not on time. In my defense she never (in two years) gave me actual requirements for data analysis or dead-lines. So I guess it all was just pure miscommunication that was not solved on time. At the end of reference she wrote that in order to avoid such mistakes I should communicate more with my future supervisor and complete all tasks in time.
My questions are:
a) is it such a bad reference and situation as it seems to be?
b.1) is it likely that a very good reference from another internship supervisor will outweigh the image to my benefit?
b.2) Shall I still include reference if it is lowering my profile?
c) is it better to ask a reference from another lab colleagues and not include reference of my supervisor at all? Most likely it would raise a question why I am not providing a reference from my former supervisor instead :(.
d) shall I send only one reference?
It is such a pity that I can not rejoice the great deal of experience I have accumulated during two years work with this supervisor because it seems to be more as an obstacle rather than a step closer to my further academic career.
Thank you for your answers in advance!