When you craft the system will take resources from the machine’s inventory first and then your personal inventory. If there is a distribution of input colours then the output will select an output colour by sampling the input distribution.
For example, if there are 75 red gleam and 25 blue gleam, then there is a 75% chance that all the outputs will be red, and a 25% chance that all the outputs will be blue. It’s a single roll for all the outputs.
I would imagine in this case the system pulled in some other colours and they were unluckily selected as the output colour.
We have discussed in the past changing this system to select the output colour for each output item. This would mean that instead of getting 100% red or 100% blue, you’re more likely to get 75% red and 25% blue.