Logical indices of observations used for each tree are stored in the OOBIndices property. This property wouldn't tell you though if an observation is sampled multiple times for the same tree.
If you need access to that info, your best shot is to introduce another property in the TreeBagger class to hold numeric indices of observations used for each tree. Take a look at line 1945 or so that should look like this:
idxtrain = weightedSample(s,w,fboot,sampleWithReplacement);
You just need to store the idxtrain array for each tree. I would add another output to the loopBody function and modify the call to loopBody accordingly.
I wouldn't recommend replacing compact trees with full trees. This is harder and would blow up memory consumption.
