Yup. There are numerous examples of the founders passing laws that appear to directly contradict the constitution. The Coast Guard traces its enforcement authority to the Revenue Service Act of 1790, which allows US officers unfettered access to vessels in US waters without a warrant. This law has been consistently upheld because judges make the lazy argument that, since it was passed by the same Congress that wrote the 4th amendment, it’s obviously compatible with the 4th amendment.
A far more likely explanation is that it was a new government based on a new constitution and everyone was still figuring out how it all worked and, in the process, they made some mistakes. Now we’re stuck with bad laws because of founder worship. The founders weren’t perfect and they didn’t create a perfect system. It’s time we stopped acting like they did.