ginput(1) asks the user to click on one point and it returns the x and y value of that point. There is no index since it's just one points. Then you take the x value and stick in into strt(i). Then you repeat that and put the next x value where the user clicks and put it into fin(i).
What I think you really want to do is to find out what index of your array is closest to the x value of where they clicked. Untested code:
for k = 1:1
uiwait(helpdlg('Please click on the starting and ending points.'));
[x, y] = ginput(2);
distances1 = abs(timef - x(1));
[minDistance, indexOfMin1] = min(distances1);
distances2 = abs(timef - x(2));
[minDistance, indexOfMin2] = min(distances2);
indexStart(k) = indexOfMin1; % Save index of starting time.
indexEnd(k) = indexOfMin2; % Save index of ending time.
timeStart(k) = timef(indexOfMin1); % Save starting time.
timeEnd(k) = timef(indexOfMin2); % Save ending time.
end
