I'm basing the question on this graphic. I assumed by 'vaccines' they meant specifically coronavirus vaccines, but I could easily be misreading it.
I suppose the negative numbers are effects not particularly associated with the vaccines but are presented with covid?
The graphic seems plausible enough and gets its point across, although it's a little vague or opaque. Presumably all of those are relative to normal risk values: So if for instance normally 80 in 100,000 people have a myocardial infarction per unit time, this chart would suggest 81 / 100,000 for people taking the vaccine and 105 / 100,000 for those who have covid-19. Without the context of the baseline morbidity rates, it's a little frustrating.
In many cases, you'll be having a lot of these due to an adverse clotting or inflammatory event. Any condition ending in "-itis" (arthritis, gastroenteritis, pericarditis, conjunctivitis) is an inflammatory condition. A lot of the others are, or are heavily associated with, blood flow problems which clotting or inflammation would likely affect to some degree.
One would have to point out that when a vaccine is injected, it dumps in a finite amount of material that will be cleared, so the immune response is likely to be pretty short. Infections, however, are due to things that replicate, so they'll stick around longer. You'll probably have covid for a week or two at least, and that suggests a great deal more inflammatory and immune activity, so it's very rational to suspect any risks from inflammatory and immune activity could be increased compared to a vaccine.