The rust indicates that the parts were not properly passivated. I suggest a QC inspection of your passivation vendor.
A passivation standard suitable for this alloy is QQ-P-35C, Type II (a warm nitric acid + sodium dichromate solution). ASTM A967 also includes some citric acid solutions.
1) If rust existed prior to passivation, the parts were not properly cleaned. See QQ-P-35C, paragraph 3.2 which explicitly requires the removal of all rust.
2) If the rusting occurred after passivation, something was wrong with the process quality (cleaning, passivation, rinsing, drying). An additional chromate treatment is sometimes specified for martensitic SS such as 416 – see paragraph 3.5. Also note: QQ-P-35C requires rinsing in clean water ( < 200 ppm TDS is required, but I use DI water) and thorough drying.
For the rework of the parts, if the rust is light and there is no grease or oil in the holes, clean with warm nitric acid, then verify that the re-passivation is done properly. QQ-P-35C, paragraph 4.6 calls for increased inspection of reworked parts.
Hope this helps,
Ken