I would do something like this for the plot:
D = load('localcombi.mat');
localcombi = D.localcombi;
[Ur,~,ix] = unique(localcombi, 'rows'); % Unique Rows
k = accumarray(ix,1); % Counts
Counts = table(Ur,k,'VariableNames',{'Unique_Rows','Count'}); % Results Table
figure
stem3(Ur(:,1), Ur(:,2), k) % Results Using ‘stem3’
grid on
xlabel('Column 1')
ylabel('Column 2')
zlabel('Count')
I am not certain what you want for the plot. This is the only way I can think of (other than scatter3) to present the column coordinates and the numbers of each unique pair.
.