Vague symptoms, such as feeling unwell, headache, cough and the flu itself are routinely blamed on having the vaccine. The time course is also often irrelevant; the vaccine seems culpable for every ailment from the moment of the jab for at least the next six months.
So what is the evidence? Tens of millions of flu vaccines have been monitored world-wide and the most common side effect by far is arm pain (64%). A small percentage also get a mild flu-like illness lasting not more that a few days. In the old formulations diarrhoea and vomiting was also reported. A handful of serious reactions have occurred, numbering under 20 in the total 2.5 million of a study I looked at (JAMA. 2005;294(21):2720). They include types of paralysis, allergic reactions, and asthma flares. All are more common with the flu itself compared with the vaccine.
So, what is the reason for the over-reporting of problems from patients? One reason is the fluvax may not work in the way that the patient expects. The flu is one of many different viruses causing cold symptoms every winter. The patient may get infected by a different virus, when they expected to be free form all colds all winter; a classic case of mistaken identity. The patient may also get the flu despite having had the vaccine. The effectiveness of the vaccine at preventing the flu is around 70% (but if you get it, it is usually not as bad).
The last big reason for this I see is that having a fluvax is a memorable event. People love to blame illness on tangible factors and a needle in the arm in a clinic is one of those (and one many would happily avoid if they did not feel was worthwhile). Maybe is easier to blame this than a respiratory droplet passed from a stranger walked past, or a mild depression related to loneliness in winter.
This may change on the horizon – many countries now give the flu vaccine up the nose. This may be generally a bit more acceptable and less foreign for us – allowing what should be viewed as routine live taking vitamins to exactly that.