I've had a 90% failure rate on what was supposed to be the final prototype before production. Turns out they hand-soldered the batch because the proto run was (obviously) only a dozen units - and some parts were just too tricky to reliably hand-solder.
I understand the logic as fully-automated assembly has a nontrivial startup cost, but a big reason of doing later prototypes is evaluating the manufacturing process as well. If the assembly method used doesn't match what I can expect in production runs, what's the point?
Weirdly enough the batch before this was totally fine. In the end we did get a massive discount on the hand-assembled run and managed to do all the testing with the one prototype we got working with some small rework, but it still cost us quite a lot of time and money. We would've happily paid a significantly higher fee to have them just do it properly - per-prototype cost is pretty much irrelevant during development.