[2019] I am now positive Calia (The collector farmhand) is not functioning properly

Note: There's no advantage to having "two breeding pairs" breeding will only occur for one pair each time. The additional slots were always intended for progeny, so you're just denying yourself 2-3 trait offspring.

I've had a look over the code and I cannot see anywhere where anything could be going wrong. It should function as expected, however breeding happens on the following conditions:

1. Have the animals actually successfull bred? The collector doesn't speed up breeding rates or offer any improvement on breeding chance. She is included in mitigation checks. Make sure you're not just being unlucky (check animals are well fed and healthy, make sure that you're allowing ample time for breeding. Mitigation is FIVE failures, which means it can be a good while before you'd be lucky if you are using animals with a long breeding cycle).
2. For the collector make sure you have beans to cover the cost of each animal. If you don't have the beans, she won't store them.

If BOTH of these situations are absolutely true, then I need you to submit a bug report using the in game system and give as much detail as humanly possible. It means that something odd is going on in the code that I can't spot on an initial investigation and it might be some odd specifics with your animals or farm set up which is causing it. A bug report will give us that information.

In the example given in the post it honestly just sounds like bad luck vs good luck, but I will need actual data from a bug report to be able to investigate any further.

It will look for a male and female pair and breed those. The pair is randomised each time so it slightly alters the range of offspring, but it doesn't increase the rate at which it happens. It doesn't take best breeding chances into account though, so you actually reduce your probability of offspring in this scenario. It's generally better to remove excess animals and focus on a preferred breeding pair.

You should have all of the ones it would have given you. So it should account for the whole time. If that is not happening, include that in a bug report as it helps us narrow down where the problem lies.

Collectors only take the ones they would store. If you have 2 slots free normally then those will breed as normal.

Please send a bug report with as much data as possible using the in-game reporting system.

No, it will not have the shiny trait included. You'll need to breed normally for the collection log.