Because it's the FA Cup and has never been any different.
Little teams raise their game and big teams get scared a bit.
True, Yeovil not undeservedly have a bit of a reputation though and if you turn up expecting to walk over them you will probably lose - I have a feeling LVG didn't know quite what to make of Yeovil but was wary of their reputation hence the slightly unusual substitution which worked in the end.