Landing a multi-target spell on two or more champions will only yield one Spellthief proc
Example: I use Vel'Koz Q. The Q splits and hits both the enemy ADC and Support. I only get 8 gold opposed to 16 (One proc opposed to two)
Additionally: The Spellthief's icon above the ability bar will sometimes not show the number of Spellthief charges you have have remaining.