With about 1,600 miles of Litchi autopilot missions under my belt, I have taken the liberty of awarding myself an honorary doctorate degree in Pure and Applied Litchiology. Donning my conical thinking cap to ruminate over the predicament you have described, my initial hunch is that you may have accidentally set a waypoint altitude lower than the obstacle in the flight path.
Plotting complex 60-waypoint missions lasting 22 minutes, I have on occasion entered negative altitude waypoint altitudes that I only caught during pre-flight cross-checking during which I closely scrutinized each waypoint in turn. If the mission you flew was not altered in any way, yet the tree still got in the way, it is also possible that the margin of altitude error you allowed was too slim, meaning that you programmed the drone to fly a tad too low above the tree canopy in your area.
To illustrate Litchi's altitude inaccuracy, the altitude callouts at my landing point have varied from 10 feet AGL to minus five feet BGL (Below round Level) ha ha. With that alarming variability in mind, I always make sure to allow at least a 20-foot clearance above all trees along my intended flight paths. May the force be with you, and may your drone never encounter a flying Tic-Tac or triangular TR-3B.