Wrong bundle discount is being applied. Why?
Bundler applies bundle discounts by bundle priority, meaning that it first tries to apply a discount from a bundle with the highest priority and so on. So what is probably happening here is that you have some of the products in more than just one bundle with the same priority.
To resolve this issue, all you have to do is set the highest priority to the bundle with the most products and a lower priority to the one with less products.

We also have a feature, which allows you to bypass this priority and just prioritize bundle discounts based on the bundle widget from which the items were added to the cart. This feature can be turned in Bundler > Settings > Discount modes.