I had a ct scan and they found a 3cm cystic lesion in my spleen that for the past month or so has been causing minor but frequent pains/ aches. also i have swollen lymph nodes on my left side neck. could someone give me a reasoning behind this?

It is not feasible to provide a meaningful opinion without additional history, physical examination and may be some tests. Splenic cyst is unlikely to cause symptoms. lymph nodes watch and wait - You may feel the nodes every couple of weeks, if any of the lymph glands doubles in size, becomes painful, ulcerates, or other nodes become enlarged, or you develop fever, or lose weight, see a doctor.

You need to see your doctor. Your question needs a lot more details, so see a doctor in person who can consider the entire picture.