This kind of substitution happens all the time with manufacturing in countries outside of your own. Any one familiar with manufacturing in China, particular circuit boards, will know after the mistakes in the first run to always state in the manufacturing agreement "No Substitutions". Other wise you will get very subtle changes that while they look the same or perform the same are not what you spec'ed.
The only other thing you can do is ask for the first 100 of the production run, not the engineering / sample run, to be shipped via air and the rest stays at the manufacture. This allows you to test will the rest is still being manufactured.
For example we had a run of 1600 boards in China, we did not state no substitutions on the agreement. The engineering samples were perfect, the production run was not. Fortunately we had the first 100 sent via air express so that we could check them and it turned out the the serial connector had been replaced with one while functional the same was actually inverted and shorter then our design. Once the shroud was placed over the board in our units the cables could no longer connect to it. We managed to catch them half way through the second 100 and got them to correct the problem.
These simple things would only come with experience and will not mitigate all your problems but does reduce some of your liabilities. They will know better the next time round.