LDO issue for atxmega32e5 powering
Looking at your schematic you have pin 1 of the uC (GND) connected pin 32 (AVCC). You have created a short between GND and the output of the LDO via the 2 inductors (or ferrite beads).

It is simple to prove this: remove "Inductor uC" from the circuit, and the output of the "LDO uC" should be 3.3V.

The solution is probably to lift (disconnect) pin 1 of the uC and use some fine wire (mod wire) to connect it to GND somewhere else.

It would make it easier to refer to the parts on your circuit if you used a standard way. Rather than calling the LDO's "LDO 3.3 circuit" it would be better to call them U1, U2, U3 etc. Inductors are always called L1, L2. Ferrite beads can be FB1, FB2. Capacitors are C1, C2, etc. Connectors are usually K1, K2.