Most of these interchanges you folks are speaking of as "puzzling" are completely unfamiliar to me; I live nowhere near them. So I don't know if this would be relevant to any of these specific cases, but people are sometimes puzzled by the presence of, for instance, the large cloverleaf interchange in Leland, MS, which during its first years served a junction of highways that maintained more than two lanes in only one direction away from the interchange.
The case of the Leland interchange, therefore, may or may not be similar to any of the others mentioned. But the reason for that interchange, as I remember hearing it explained on the radio years ago on a WJDX public affairs program, was a high accident count at the previous intersection. The safety of both US 82 and US 61 in Mississippi was substantially enhanced simply by removing all left turns at that accident-prone junction.