When we placed a unit into production that included high pin count connectors, we discovered that the I/O connectors did not fit properly. This was odd, in that many units had been built successfully by our prototype vendor, and there were no changes in this area between the two designs. What had happened?
It turned out that our PWB geometry was slightly off on the connector hole pattern. The prototype shop noticed it, compensated for it with some emergency tooling to spread the connector pins, and assembled the units. A little hand labor, and the connectors fit. This allowed the connectors to be inserted, but under some stress, likely damaging the thru holes. The ability to withstand temperature cycling was certainly degraded, and they all would have failed in the field after a short time.
The prototype house never notified us of this issue. They simply delivered the boards, and we powered them up and they worked, so the problem was not found. Our temperature test was only a few cycles, for functionality, not for reliability.
This required us to change the PWB artwork to correct the connector pinout pitch (again). This problem would have been found if we had built the prototypes at a full scale production house, who would have complained about this, perhaps not done it at all. A additional PWB turn to fix this problem would have been avoided.
Of course, a full scale production house will hold you up for dozens of reasons are irrelevant to the purpose of the prototypes, setting your integration schedule back. Pick your poison.