Yeah since you took the Engineered Evolution Ascension Perk, the other two (Mind Over Matter and The Flesh Is Weak) become unobtainable in that save game
That has been a thing since Ascension Perks got added in 1.5 alongside Utopia
"Ascension perks have 3 major paths that are exclusive. One path focuses on psionics and establishing contact with The Shroud, a second path focuses on biological mastery and genetic modification, and the third path focuses on turning your species into fully synthetic androids"
If your game didn't have iron man mode enabled when you started it up, achievements/trophies are disabled by default
If it did have iron man mode enabled then this would indeed be a bug [unless you didn't do what the trophy required]
looking at the trophy list, there are 3 separate trophies, 1 for each of the routes with specific requirements
Beyond the Veil - Breach the Shroud : You need to be a Spiritualist empire to even get the Psionics tech to show up, but you need to complete the special situational log after you get the Transcendence AP. You should get the trophy either once this is done or after your first contact with the entity known as The Shroud
Like Tears in Rain - Evolve into perfect, immortal machines : You can get this on any empire type that isn't Spiritual as long as you have the right tech researched [Robots>Droids>Synths>Synthetic Leaders] and then you finish both the The Flesh is Weak and Synthetic Evolution situational logs once you've gotten the appropriate AP unlocks
Controller Evolution - Genetically modify a species to possess traits worth 7 points : Once you've reached the right tech and gotten both the Engineered Evolution and Evolutionary Mastery, you'd have to go into the people tab, then species and then choose a species in your empire (recommended is use your main species) then just give them positive traits. Each trait has a point value, so fiddle around with it until you find a combination that nets you at least the 7 point requirement
