Yes, as you mentioned this has to do with the little endian bit-order in Qiskit. Most textbooks (and the first matrix you showed) are in big endian order.
If you want to know more you could check out these posts/documentation:
If you want to convert your Qiskit circuit to big endian you can just use the reverse_bits
method:
from qiskit import QuantumCircuit
from qiskit.quantum_info import Operator
circuit = QuantumCircuit(2)
circuit.cx(0, 1)
print('Little endian:')
print(Operator(circuit))
print('Big endian:')
print(Operator(circuit.reverse_bits()))
gives:
Little endian:
Operator([[1.+0.j, 0.+0.j, 0.+0.j, 0.+0.j],
[0.+0.j, 0.+0.j, 0.+0.j, 1.+0.j],
[0.+0.j, 0.+0.j, 1.+0.j, 0.+0.j],
[0.+0.j, 1.+0.j, 0.+0.j, 0.+0.j]],
input_dims=(2, 2), output_dims=(2, 2))
Big endian:
Operator([[1.+0.j, 0.+0.j, 0.+0.j, 0.+0.j],
[0.+0.j, 1.+0.j, 0.+0.j, 0.+0.j],
[0.+0.j, 0.+0.j, 0.+0.j, 1.+0.j],
[0.+0.j, 0.+0.j, 1.+0.j, 0.+0.j]],
input_dims=(2, 2), output_dims=(2, 2))
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