Bad reference VS no reference 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!
The bad reference is given to prevent you getting the position, it is a warning to whoever might supervise you. From what I have seen, it is quite common for far more subtle and hidden negative messages to be put into an academic reference than what you have described. In these cases the references are not used because the letters are there to convey a warning. That's not to say I know the right answer, but my feeling is that a bad reference gives you no chance whereas a single good reference gives you at least a shot.