I've been thinking about making a thread about this, but:
1) Pluto/Setsuna is given two different stories in Infinity. In Act 32, Pluto says she was reincarnated thanks to Neo Queen Serenity, who lent her her power. But then in Act 33, Michiru (who I believe is the one speaking) suggests she, Uranus, and Pluto were all reincarnated on Earth along with everyone else following the collapse of Silver Millennium (the artwork supports this). WHICH IS IT?
2) Like you said, in the BMC arc there's much ado about Pluto's not being allowed to leave the Door of Space-Time. But...why? Diana, a helpless kitten, is able to take over Pluto's job (however briefly). When Pluto "dies", no one seems at all concerned about who will guard the door. Literally no one but the Sailors and Tuxedo Mask ever seem to visit the Door. King Endymion himself says only people who are from the Moon Kingdom are able to approach it, and we never see any villains attempt to go through it. In fact, that the Black Moon Clan found another way to travel through time seems to render Pluto's whole job and the whole concept of the Door pointless. Pluto's role/responsibilities are further made ridiculous when you realize that she literally gives away Time Keys to almost every character she meets. Not only does Pluto's job make zero sense, she's also incredibly bad at it.