I was a bit put off by the name of the new ugin the ineffable... there has only ever been one other character with that same epithet; yawgmoth. could they be the same individual from different time-periods? my understanding is that ugin's smart enough to deal with time travel, and maybe with the advent of the elder spell, something something, he becomes yawgmoth..
or maybe its just an honorific bestowed to ugin without any bearing on phyrexia or yawgmoth at all.
nah couldn't be that
karn and teferi team up to send ugin back in time to build a weapon to stop the new phyrexians, but they send him too far back and that weapon turns out to be the actual phyrexia. he dies at its heart realizing he's no better than his brother. we all finally move on with our lives.
Tl;dr I am not bothered by this very much, but I sympathize with people who are. Yawgmoth is one of the defining characters of Magic and I could imagine that infringing on any part of him would be a sore spot for other fans of his. (I personally regard him as a favorite villain but think he's completely, indefensibly evil.)
Ugin, let's be clear, is definitely not the Dragon-Planeswalker who created Phyrexia. That person died before Yawgmoth and Dyfed visited the plane for the first time, and left a corpse, which had to have been destroyed when Phyrexia was. We all know that Ugin's not really one to let a little thing like death get in his way, but he also left a corpse in a different place at a different time - as the fossilized Nexus of Tarkir in the original "Khans" timeline. (Also, we're told that Phyrexia's creator was evil, and left to think that the essence of the world was inherently evil, which was part of why Yawgmoth was able to successfully build it into a Machine-Hell.)
First, I don't see "the Ineffable" as a title that belongs solely to Yawgmoth. It's not like Ugin is being called "Lord of the Wastes" or "Father of Machines" - it's not as though it's either a creative infringement/error or that he's somehow taken up the mantle of Yawgmoth, like Karn did with the latter example while under the Praetors' corruption in Scars block. While "Ineffable" was indeed one of Yawgmoth's epithets, it's also a generic descriptor - both Yawgmoth and Ugin have motives and natures that are beyond the understanding of lesser beings.
Second, card names don't necessarily exist in-universe; they're bounded by the narrative of the Magic story, sure, but they're not necessarily what people call the characters they represent; some of them really exist in order to, well, have different card names than previous versions because new designs need new names. While Karn, the Great Creator is in War of the Spark as well, that doesn't mean his planeswalker colleagues during this storyline would ever address him as "Great Creator". In fact, they'd most likely just call him "Karn", or if someone like Koth, who would revere him for some reason (as the creator of Argentum, perhaps), were around, they might address him as "Lord Karn", but that's about it. But, obviously, every Karn planeswalker card can't just be named "Karn". Planeswalker card names have to convey a sense of who the character is, but they needn't be spoken by anyone within the narrative.
So Ugin, the Ineffable is called that because he's lowercase-i ineffable. Yawgmoth is called that because he developed the epithet within the story of capital-I "The Ineffable", and also because he's that actual adjective.