I am not an expert on this subject, by any means, but I suppose that freediving, like any sporting activitiy is good for your hart.
When I was still a competitive swimmer, I also had the problem you describe, but the doctor told me that it is not the heart that you feel, you actually feel some muscles in the ribcage, as it stretches a lot during training/ heavy breathing.
Anyway, this is too important to speculat, so I would deffinetly sugges that you go to a doctor, decribe the simptoms and do some tests, so that you are shure, that you do not have some kind of heart condition.
best of luck,
Aljo