A pimple will become inflamed and the damage that the immune system does to the skin will determine the level of fibrosis and other structural damage and abnormality which makes it look especially icky, and so fish oil's anti-inflammatory properties will improve that by reducing the ongoing inflammation. It will look less red and be less severe. There's no mystery there.
Fish oil is susceptible to lipid peroxidation, though, becoming oxidized itself and oxidizing cell membranes, so that can make things worse. There is some evidence that "omega-3 skepticism" can be based upon like large doses of fish oil causing damage to the body, but where I disagree is that this means that polyunsaturated fats are inherently damaging. The right kind of vitamin e may prevent lipid peroxidation and thus improve the efficacy of omega-3s in playing their part in health. Fish oil with the usual low amount of vitamin e compromises vitamin e status, increases lipid peroxidation markers and is only mildly effective at doing what it usually does. A high vitamin e fish oil (or diet I'm guessing) doesn't alter vitamin e, doesn't alter lipid peroxidation markers, and is far more effective in improving certain biomarkers http://www.ncbi.nlm.nih.gov/pubmed/1995786 Most people are deficient in vitamin e as it is! I'm certainly skeptical of the advice that everyone should go out and buy fish oil without thinking and take a bunch of it. And I would guess that fish oil might be bad in that low vitamin e context but it has its uses and appears to be safe under conditions of high vitamin e levels. Although it uses up vitamin e so however much one needs is all one should take. (however much that is)
How much are you getting? 1-2g through food is normal on a paleo type diet and then one might not need fish oil at all, although since you have seen improvements you might not have been getting very much to begin with. Just make sure to get plenty of vitamin e, choose a good quality product, and don't go overboard on it.
Also I think that the supplement pantethine is really good for acne. I used to get pimples, and they got a lot better on a paleo diet but never fully went away until I took pantethine. I don't really know how to explain it but there are lots of anecdotes of successes with it. Maybe since pantethine becomes coenzyme A and CoA metabolizes lipids it helps transport sebum so it doesn't clog the hair follicles. Big guess, not sure if it's right but it works for me.