Bailey,
Don't look at the C25K as a strict schedule, use it as a guide. If you have other activities, just adapt C25K around your life. It is OK, it will not yell at you and nobody will know.....
The same goes to your problem with knees and joints. Try to ease up the load, go slowly and/or shorter distance. Take two days rest instead of one. See if it helps and pain is gone or subside. If it is not, then check with your doctor. Otherwise try slow increase the load.