Why could yoga be giving me joint pain and aggravation?

Too much too soon. Your body is giving you feedback in a big way. If we're not used to stretching, new positions, exercising for a length of time, we can get real sore real fast. Modify your yoga. Good position? Maybe not stretching as extremely. Cut down on the time. If you're not sore the next day, then you're ready to progress. Here's a high five for getting out there and getting moving.
Because. Some yoga movements and positions do put a lot of stress on some joints, and people with arthritis will be effected. Also those with lax joints can be sore afterward. Try to avoid those that are specifically bothersome and continue with the others.