it could just be your body getting over the shock of the extra running, it could be bio mechanical. Do you have proper running footwear? That will make a big difference.
May be worth getting gait analysis done before it becomes a bigger issue. If you have pain then Drs or physio.
As with any new activity various bits will complain at some point so maybe look at the strength and flex program as well?
What you're feeling in your knees is a message that's telling you that your running is putting some strains on your body (which is to be expected). It's worth doing the recommended strengthening exercises alongside C25K. I did these and after a week never felt anything in my knees since.
Long-term running will strengthen your knees and only ruin them if you persist in running multiple marathons every year. That is if you have appropriate footwear. Follow the link in the guide about shoes if you have any doubts about how well you are short.
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