Steven Miranda wrote:
...doing something incorrect, like the front foot turned out too much and your knees pointing out, etc.
I am not familiar with the Yoshinkan basic exercises, but this caught my attention. Your foot should always be in the same line/plane with your femur when you are bending your knee and putting weight into your foot. I have seen people turning the foot way out or in in relation to the line of their upper leg then cranking their weight into it as some kind of supposed warm-up/stretching exercise and it makes me cringe. Just because you can twist, pull, or stretch your body into a position doesn't mean you should. Ankle flexibility isn't necessarily a good thing.
Given the amount of months training mentioned, the problem could also be simple overtraining. It usually takes a few months to build up to tendonitis and other white tissue problems. If you were not particularly athletic beforehand, you may have just added too much stress too fast. A general training increase rule is "the 10% rule" - don't increase loads more than 10% per week. This would be difficult to apply to Aikido, but if you went from nothing to training 3 or more times per week, you probably violated it.
Another possible issue is that your leg might not be stable and strong enough to do all that you are asking of it, whether it is aligned properly or not. If this is the case, you may need to lay off or stop Aikido for a few months and focus on strengthening exercises - particularly squats and lunges, without any added weight at first... remember the 10% rule. Transitioning into something like this should be part of your rehab anyway.