Only one side of the transformer is fused.
It's a 18VCT transformer, right?
Why ferrite bead supply the MCU? Do you know you'll need extra filtering between, whatever else is on +3.3V? Or filtering to, as the case may be? It can be better without, as the supply is bypassed by everything connected to it. This is more helpful on 4+ layer inner-plane PCB designs, but doesn't make much difference on 2-layer designs with only stitched ground fill (where +3.3V has to be routed as just any other trace, and so there isn't direct communication between bypass caps on the supply).
As above, large inductors on linear regulators, is just wrong. Easy fix.
If you're going to the trouble of burning three separate MCUs, why not consider probing the supply voltage with an oscilloscope while you blow one of them? Set it to rising trigger, 2.5V threshold, single shot acquisition, scales around 1ms/div and 1V/div, and see what's happening. As thm said, this is probably better done without an MCU (and other chips for that matter) installed, so you aren't burning up your supply of parts...
Tim