Sore Ankle from Cycling

I am a budding triathlete and pretty new to the bike. I tried out a friend's bike last summer and found my left ankle (really the top of my foot where the ankle and foot meet) was getting very sore for a day or two after the ride. I found that the pain went away completely when I stopped riding the bike altogether. Since then, I have gotten my own bike which is more suited to my frame. I have found this pain has come back and again seems to persist for one to two days post ride. Unfortunately, I am in enough discomfort to require missing running workouts. I don't really have the luxury of missing runs now as I gear up for a half marathon in May and my first Olympic distance Tri in July. Does anyone have a suggestion for what i can do to remedy this issue? I think going for a true fitting may help to align my foot better on the pedal or perhaps pedaling in a lower gear as i get my muscles acclimated to cycling but i am just curious if anyone has experienced this type of pain and/or has any suggestions. Thanks