Are these just side effects of missing birth control pills or something else?

Patient: So I’ve been on this birth control pill for a few months now. Ive missed a pill before but I took two the next day and nothing happened. This month I finished a pack and my period finished on my last “Inactive” pill. But I forgot to get my new pack and missed the first day of it… I took two later the next day ( I usually take my pills about 11:30 in the morning) So I missed one. Then the day the after I took two I took my pill late, (about 10 hrs late). The next day I had sex a few times. And I felt fine till about 3 days after that. Now I’ve got headaches, cramping, lower back pain, nausea, mood swings, been very tired etc. I don’t feel sick, like a cold or anything. So I dont know if this is from messing up my pills the first few days or what? I know the first week of the pack is important. So Is it just side effects from the pill or could it be something else?

Doctor: