I'm not sure that there are production issues so much as a error on the part of the sales department in predicting the customer demand. The sales people predict customer demand and estimate the number of sales. This info is used to order components, set aside factory space, reserve shipping, its a huge chain of preparations for production and some items are long lead and difficult to speed up deliveries. Its even harder when you are introducing two new models at once. They obviously share some of the tooling and components so do you rob one to provision the other?
With camera sales slowing down, and Canon as well as other manufacturers having to drastically lower prices due to overstocks, they were likely very conservative at provisioning for the new models. The R6 was expected to be the biggest seller, so a lot more of them hit the pipeline.