I think it would be nice if you could set a preference to turn overlapping time entries on or off (some of us never want this to happen). If you have an entry that breaks that rule, just have an option for that entry that says “allow to overlap with other entries” or something like that, so you can do a one-off exception.
Also, would be nice to set the default minimum time increments. My company makes us track in .25 hour increments. If the app could force that, so nothing is less than .25 hours, that would be helpful. Others might prefer .5 or 1 hour increments. Setting that in the prefs, as well, would be very handy.