Bug or feature
If it is a bug, it is almost impossible to debug since initial stuck boards are insanely rare. I have been playing for 563 days and it has only happened once.
80%+ chance
@Little_Infinity, and others, have shown, with computer simulations, that initial matched boards are very common ( reportedly 80% ). So it is easy to bug test.
Shuffle code
The Shuffle code is also used for Tornadoes, and Hurricanes, so allowing Matched boards to result from a shuffle appears to be intended.
Notes
FIN