X = cell2mat(cellfun(@max,Zeit_Flutende_10000_BA,'UniformOutput',false))
Note that you have at least one empty entry, for example, the third row of your cell array. This will be deleted from the output, so you output array of doubles will have less rows than your original cell.
Also if you just remove that empty row everything gets much simpler because we don't have to keep a cell entry for the empty result and we can use the max function to directly get a matrix of doubles, so for example:
Zeit_Flutende_10000_BA(3) = []; % remove the third row
Zeit_Flutende_10000_BA = cellfun(@max,Zeit_Flutende_10000_BA)
