I suspect it's difficult to tell as this is flu season. I started OP about two weeks ago (with excellent results); but I will say I too suffered from a sore throat for the first week. However, my daughter was home sick from school at the time and one of her symptoms was a sore throat, so I do not know the origin of mine. I treated my sore throat by gargling with Colloidal Silver ; I also tried putting droppers of tobasco on it and I ate fresh minced garlic by the spoonful (with a water chaser). Many people use cayenne pepper on sore throats with good success, but I was out of Cayenne, hence I used tobasco. As for difficulty swallowing, I didn't really feel that, but I have noticed that OP pulls a lot of crappola out through the nasal cavity in the back of the throat, that can make you feel clogged and choked.
I had strep throat when I was younger and from what I've read these viruses can sit dormant and then become active again. I think the oilpulling is trying to pull out the virus and get rid of it. In that case it may hurt for a while but as the oilpulling doctor said when it gets worse it's a sign of healing. I rarely get sore throats anymore but when I did a clove of raw garlic on whole grain or sprouted bread with olive oil took it away within a half hour. It kills the strep virus and many others. I hope this helps.
One possibilty for why you have a sore throat: olive oil can cause a burning sensation in the throat if it is high in oleocanthals.
"Inspired by a tasting experience at a molecular gastronomy meeting in Sicily, where he noticed that high quality olive oil produced a throat-stinging sensation similar to that caused by ibuprofen, Beauchamp and his team analyzed freshly pressed extra-virgin olive oil and discovered a compound that suppresses the prostaglandin system, the same pain pathway as non-steroidal anti-inflammatory agents, such as ibuprofen.
Although its chemical structure is quite different from the anti-inflammatory compounds in non-steroidal drugs, olive oil's anti-inflammatory component, which Beauchamp named "oleocanthal," has a similar effect.
Scientists believe this finding is significant because inflammation plays a key role in a variety of chronic diseases."Some of the health-related effects of the Mediterranean diet may be due to the activity of oleocanthal from premium olive oils," said Beauchamp."
In addition to what others have said, a few things --
1. Lots of people have reported sore throat after beginning to OP. I'd say it's a fairly common detox reaction, especially at the beginning. I had it (I also had sinus congestion problems, with which OP has helped almost entirely! w/in a few weeks...) too. Many report cold or flu-like symptoms and that is "normal" around here. Part of your sinus congestion may be a low-level infection that sits around in your head cavities -- sinuses, around ears and throat -- and this could be "coming out" -- at some point you might want to add a few drops of the anti-microbial oil of oregano to treat this, although I would recommend waiting until you are OP'ing with no other strong detox symptoms like the sore throat you have now.
2. Olive oil, over time, can/will give your teeth a kind of chartreuse cast. My mom gave us a half-gallon of OO last year and I used it for a while and definitely noticed this. It seems to be the only oil that does not have that tooth-brightening effect. Just FYI, but especially with Kebod's info on olive oil's potential to cause irritation, it might be time for an "oil change" to sesame or sunflower or coconut, etc.