The use of cement mortar as filler on historic timber-frames is commonly seen but it is wrong and destructive. It is a short-term fix but leads to longer-term decay of the frame, moisture absorption and can create a habitat for beetles. It also looks unsightly.
There is no option for repair other than carefully removing it, to allow for an inspection of what is hidden so that a decision can then be made about what to do.
It might be possible to do a specialist oak-frame repair or perhaps to use an appropriate lime filler instead. Seek advice from a conservationist before doing anything.