A recent Shopify update has affected how discounts work, which mostly just made it so you can't stack multiple discounts on the same item. Since I like letting people stack discounts, this has changed how I run sales/what kind of sales I can do.
TLDR: Annoyingly, Shopify now allows only 1 discount per item.
Under the old setup, different discounts like bundles and BOGOs could be allowed to stack with each other.
Under the new setup, you can't get multiple item discounts on the same item. The lesser discount is cancelled.
The only discounts you can stack currently are order discount codes, the kind that you put in the coupon code box at checkout. I'll be doing a lot more of this type of sale in the future instead of automatic ones for this reason!
The discount that doesn't work great under the new system is Freebies: it still works, but it can remove the discount on another item if everything in your cart is already discounted from another sale.
Freebies are coded as BOGOS because there is no 'free with purchase' type code. It's 'buy anything in the shop and get an item in this category free'. This means it attaches itself to another item, and that item will lose a smaller discount like a bundle discount, because the freebie discount (100% off) is higher.
I'd rather leave it because most of the time this condition doesn't happen and all the discounts work together. You can also get around it by splitting up orders like you already can if there are multiple patterns in the freebie section :)
And of course, if you need help, just send me a message through the chat box!