It may not be a glitch. BE (and domestic FC) fares are dual-inventory fares (their fare basis codes start with a coach fare class) which makes it virtually impossible for fares to get "upside-down". Since the fare you get with dual-inventory fares depends on both coach and booked class inventory, if there are only seats available in higher coach classes, you will also only get higher fares in the other classes of service as well.

Airlines do not always use dual-inventory fares on international PE fares, so there is not necessarily anything to prevent BE/Main fares from getting inverted with PE. Although looking at AA PE fares to the EU, I see they use dual-inventory fares for PE fares here as well (DL and UA do not). So this may be due to some kind of inconsistency in the fare rules (perhaps unintentional) between Main and PE fares. Dual-inventory only prevents fares from getting upside-down if you have matching PE fares for each Main fare with the same fare rules. Sometimes, they can screw up and have outlier fares that don't match.

Also, when searching for roundtrips like above, you can't assume the itineraries are identical for the fares shown until you select both outbound and return directions. The higher BE/Main fares may be non-stops both ways, while the cheaper PE option may involve a connection on the return (it may be some sort of broken fare option which is not allowed with BE/Main fares).