OK, maye some aren't quite so mysterious.
The Marie Celeste, for instance, was likely abandoned by all hands when a sudden storm blew up, which would account for the missing lifeboat. A storm might very well have sunk the lifeboat while leaving the ship untouched. We might possibly speculate that a phenomenon such as St Elmos Fire might have caused them to abandon ship in a superstitious panic.
Why shouldn't Roman jars be found in Brazil? In 1970, Norwegian explorer Thor Heyerdahl and his crew sailed from Morocco to Barbados in Ra II, a papyrus boat built to designs taken from ancient Egyptian models and drawings. We know, therefore, that such voyages were possible, and if a thing is possible, people will do it. Egypt traded extensively with Rome and other Mediterranean cultures, so the use of Roman-style storage jars for cargo or supplies is far from impossible.
As to Area 51, if I were the US military, I'd be more than happy to have all the nerds, geeks and conspiracy theorists focuing on Nevada while the real work got done somewhere they never heard of!