Some googling seems to suggest you very much can microwave flies. There are however some spots inside a microwave that don't receive as much energy, so a fly might survive if it largely stays within those points.
Besides which, microwaves don't work by electrocuting what's put inside them.
Marsstriker t1_j68it8r wrote
Reply to comment by Chromotron in ELI5: why can't we use electricity to kill microorganisms in small amount of water ? by FreshT3ch
Some googling seems to suggest you very much can microwave flies. There are however some spots inside a microwave that don't receive as much energy, so a fly might survive if it largely stays within those points.
Besides which, microwaves don't work by electrocuting what's put inside them.