Mixing up the two bases
Typical misconceptionIf the sweep is slow, the state does not change.
Better mental modelThe state stays in the same energy eigenstate, but that eigenstate changes its fixed-basis composition as the Hamiltonian changes.
Two crossings are not two coin flips
Typical misconceptionTwo passages are two independent coin flips, so their probabilities multiply.
Better mental modelThe two amplitudes stay coherent and keep their relative phase. The simulation carries that coherence through the whole protocol.
The formula is only a reference
Typical misconceptionThe exponential formula should match every finite pulse exactly.
Better mental modelThe formula assumes different endpoints, a particular initial state and no noise. The gray finite-time curve follows the evolution actually set up in the Lab.