If you are paying off the balance each month (or by whatever payment terms it is on - student overdrafts are often interest free for 3 months) it shouldn't negatively affect your credit score (at this stage anyway). I suspect the problem with the contract is that it is your first contract - you will probably have a very limited credit history which can be a negative effect for lenders as they aren't sure you will continue paying the contract over time.
That said I probably wouldn't suggest buying a very expensive phone on your student overdraft. You really want to keep that available in case e.g. you are out of money waiting for your next maintenance loan to come in and need to pay rent, or have a sudden unexpected cost. That's also a lot of money upfront on a phone.
If you need a new phone and can't get it on a contract I would suggest looking at used refurbished phones for much cheaper. Remember you're a student - you aren't really in a position that you are going to be upgrading to the latest whatever every time for the biggest cost. You need to be thrifty and get the cheapest thing that will fulfill the function. If you need a smartphone there will be much cheaper options. If you literally only need it for calling people because you have e.g. a tablet or something already which you would undertake the smartphone functionalities on usually, just buy a Nokia brick phone or something on a cheap sim only contract.