You definitely can get these symptoms when taking the pill. The pill provides hormones which effectively make your body think you're pregnant and, therefore, your body can adjust. I went on the pill (Rigevidon) about 2 months ago and had these type of symptoms, I also came down slightly ill a few days in and was considering stopping it due to flu and headaches that were likely caused by the change in my hormones but everything seems to have balanced out now.
I'm not a medical expert and I'm not saying that you are not pregnant but the fact that you still would have had time before your next period and that your sex was protected make your chances extremely slim, also the fact that the pregnancy test was negative. If you're worried you can always take a pregnancy test again in a couple of days time but in between the time that you had your last period there would be a very small chance that you'd be feeling the effects of pregnancy at this stage if you were pregnant.