Vision actually tried to explain this in the movie. Corvus Glaive stabbed him with the same weapon that was specifically interfering with his phasing. Vision literally says, “The blade. It stopped me from phasing,” and then says his systems was failing. That injury never fully healed before the Wakanda battle. By the time Thanos gets to him, Vision isn't the same fully functional Vision we saw earlier in the MCU. He's already been severely damaged, his powers have been compromised, and the entire reason the Avengers were trying to remove the Mind Stone safely was because of how vulnerable he'd become. And there's another reason I wouldn't call this a simple plot hole: Vision's phasing isn't an automatic passive ability. He has to use it. We've seen him phase through objects and people before, but that doesn't mean he can always activate it regardless of his condition. In fact, there's even deleted Infinity War footage showing Vision phasing through Corvus Glaive during their fight. So the filmmakers clearly knew exactly how powerful that ability could be. The theatrical version just established that Corvus' weapon had already taken that option away from Vision. So yeah, if Vision was at full strength, Thanos grabbing him like that would be a MUCH bigger question. But the Vision Thanos encountered was basically a damaged version of himself who had already been told his systems were failing.