The trick is to get the indices from the histogram, but unfortunately hist3 does not return the indices of the input values. Introduced in 2015b is the function histcounts2, which does return these indices. However I do not have 2015b, so I found histcn on FEX, which seems to do what you require.
I tried it like this, is three lines okay?:
nEv = 10;
posXY = rand(nEv,2);
times = rand(nEv,1);
%
[idx,~,~,loc] = histcn(posXY,2,2);
A = accumarray(loc,times,[],@(n){n});
B = cellfun(@(v)diff(sort(v)),A,'UniformOutput',false)
Where B is a cell array where the cells correspond to the bins of the histogram and contain the differences in the sorted times values corresponding to the X and Y values that were sorted into the corresponding bin. The variable A contains the time values themselves, so you can check this by hand if you want.
