I'm not allowed to talk specifics, but the engine's design is not the problem. We had no issues with this same engine in use in the LC sedans.
There was a change made in the manufacturing process when we started building them for Tundra/Sequoia that passed all of our initial preprod testing, but introduced issues when scaled up for mass manufacturing that we were not able to predict or model. The manufacturing process was changed again, and our at-scale testing shows there is no longer machining debris in the assembled engines.
Scaling up manufacturing from pilot plants to full scale usually always introduces issues. Most of the time they're tiny enough that it doesn't make a difference, but sometimes they snowball into larger issues.
Edit- also to add, a sub 1% failure rate is PHENOMENAL in the auto industry, especially for an automaker that makes 3x the vehicles as the next largest manufacturer. Ford's 2.7 ecoboost had a 4% failure rate in the first year of production and still sits around 2% across all models. GM's Pentastar V6 has sat at a 3% failure rate since their introduction.
Toyota is known for reliability, but not perfection. Across statistical averages, toyota is significantly better than most other automakers, but we still have our issues sometimes